I think an important distinction to be made is how this Spanish failure to conquer the Inca goes about. Does Pizarro fail militarily? Does the opportunity never even arise because of a gimped Spain having more limited opportunities? IMO the most important component of Inca survival is their relationship with Europeans as a collective as well as with each individual European state.
An Inca Empire that is never truly threatened by Europeans during OTL's conquest, still goes through their civil war, and is then forced to rebuild in relative isolation and ignorance of the wider world is one that's still going to be vulnerable to future incursions. And if the conquest of the Aztec + the conquest of Malaya goes as OTL, then I'd expect that they're still on the menu for quite a while. I doubt that things could go as pear shaped militarily with the worst possible timing as OTL, but it's still going to be ugly and leave the Inca as Europe's pinata from which easy gains in exchange for military force for a long time.
As an example, say the Inca after first peaceful contact with Portugal start focusing more on their coastline due to the value they find in trade. The Inca won't be aware of their own degree of need for horses and labor animals, steel weapons and armor, or firearms and cannons. The lack of military threat from these initial traders will only expose the relative backwardness of their society as a military threat to Europeans while leaving them in relative ignorance; trade is strictly on Portugal's terms. They'll cotton on to some things over time I'm sure, that's inevitable, but Europeans will still have a growing perception in their abilities to project power overseas that will be validated by every success and that will ignore every failure(see: why nobody talks about Spain's adventures in the American South or how much conquistador manpower was wasted in the Amazon because they were independent actors willing to send it for the myth of El Dorado). I'd be
very surprised if they never have to deal with a Spanish conquistador venture or the Portuguese deciding that they can extend their extortion racket(sorry, feitoria system) to the Inca and start seizing ideal ports and fortresses along the coast.
IMO the biggest pro of a failed Spanish invasion that roughly happens around the same time as OTL is that the Inca are immediately forced to touch grass and can see how close they came to losing it all to (OTL several competing) bands of loosely sanctioned soldiers of fortune. Without that immediate awareness, the Inca will return to what they know and will effectively become another Malacca, Sri Lanka, Kongo, or Aztec Empire just with a slow cook timer.
Now I am painting a pretty pessimistic scenario here and assuming the Inca will exist in complacency. Who's to say the Inca won't hear of Spanish Mexico and the details of that conquest within a decade of first contact? The Inca do have something most of these other states don't have, and that's a ridiculous degree of centralization by the standards of the day. The state serving as a social safety net, arbiter of labor and resource distribution and the isolating nature of the Andes means that the Inca are simultaneously the whip and the glue. Most of the Andes truly can't afford to go back to the before times of isolated statelets, especially in a post-apocalyptic setting that the Inca are effectively going to be living through. Unlike many other states of the time, there's sincerely social pressures that will encourage the (Andean) Inca Empire to pull itself back together. IMO that's ultimately what we saw with OTL's Inca civil war. And that's without getting into the Inca's penchant for playing with demography(see: ethnic cleansing, deportations, settler colonies, othering of non-conformance, etc.). We saw an impressive degree of homogenization for what was ultimately what, 80 years? We arguably saw something akin to the Mandate of Heaven arise in the Andes in the timespan the Inca existed and it's a concept that I think would only be further reinforced with even a mediocre attempt to repair the realm after the civil war + the rampant pandemics.
My take is that a scenario where the Inca avoid early conflict with Europeans their first wars are in the late 16th or early 17th century, they're going to get the Burmese treatment. Lose control over their ports, ultimately getting humiliated militarily, and being turned into a tributary that's paying their dues in large amounts of bullion and as a captive market now that their demography has rebounded somewhat. Truly an Emperor has no clothes moment, and I'd expect the Inca's trajectory to mirror something akin to a much less populous Japan in mentality while getting the 19th century China experience. Flirting with anti-imperialism and ideologically convenient ideologies, Emperor worship, and an obsession with restoring their own sense of dignity while simultaneously being plundered economically, militarily disregarded as any sort of threat, and seen as liable to be influenced and extorted by outside powers with ease.
On the other hand an early pants down moment for the Inca will alter the trajectory of their rebuilding after the civil war and leave them more exposed early on which is likewise more dangerous and going to leave them prone to more 'checks' by conquistadors et al while simultaneously leaving them as a competitive latecomer to the gunpowder empire club(IMO). They've got enough wealth, demography, control, and inertia behind them that I think they'd stabilize and not be in immediate danger of European aggression until the the late 18th/early 19th century akin to the rest of the world's notable states that dodged early imperialism. But with an already established tradition/glorification of 'modernization'/adopting the knowledge of others which they can(and does) harken back to the pre-contact Inca Empire and their adaptations to the different peoples and their knowledge that they in turn used to build their empire. I don't think the Inca would be as exposed or as vulnerable as the early 16th century ever again due to sheer need to Never Again any such incident.
Internally I'd expect the Inca to continue to homogenize demographically the longer that their realm lasts, and to follow a trajectory similar to China in that even the people that aren't strictly Quechuas, sun worshippers, or even politically aligned with the Inca ruler to still see value and legitimacy in the Sapa Inca, his state apparatus, the Quechua language, and the resource management the state provides. The political dynamics of this state would be up in the air of course, but assuming OTL's civil war still goes down then the asses of the Inca aristocracy are exposed and are liable to be disfavored compared to the Inca bureaucracy, the thing actually keeping the whole state running. This is why I lean heavily into parallels with China politically and Japan ideologically. The Inca are a hopscotch away from kneecapping the power of regional lords and atomizing political power to the village level; to a degree this was already true but putting most of the reigns regarding regional management in the hands of bureaucrats instead of aristocrats isn't far removed from what happened OTL. Really the biggest leap is distancing the bureaucracy from the aristocracy as a source of manpower for it. So long as the two are entwined the Sapa Inca is vulnerable to their influence. And I'm sure that the rulers of the Inca will be painfully aware of this with the benefit of hindsight after the civil war. Who were Huascar's backers? Where was their power center? If the Inca already stratify their society such that they can train dedicated metalworkers/weavers/etc. then I've no doubt that a dedicated class of bureaucrats that extends past quipu counters/weavers could and in time would arise.
I'd also expect a shift in interest to the seas, building off of both European contact/trade and the legends of Tupac Yupanqui. Growth in coastal cities would be marred by the Inca being unable to control these cities to the same totalitarian degree they control their mountain cities, but would still boom. Routes that transport silver and other metals, textiles, dried foods, building materials, and quinine for foreign trade would be established akin to the Royal Inca Road. The above would be the Inca's major exports, while in turn Europeans would trade in what we all expect; OTL's major notable goods from the Colombian exchange at first alongside weapons and armor, but I think trade would find a few dedicated niches unlike in China that found little interest in trade with Europeans. Off the top of my head, ships and in the longterm, lumber, would be a big one. I sincerely doubt the Inca will close inwards or disregard the rest of the world. Luxury goods from the rest of the world would be another; trading Chinese porcelain for Inca silver would likely be enormously profitable for the Portuguese. Artisan goods from Europe would likely see a steady trade as well, from clocks to wine. I'd expect the Inca to in time build up their own local industries but the Europeans will have a good window of time for reliable trade. Though I think what the most reliable trade good would be is ultimately slaves. The Inca are in a manpower crunch, and guess who just specialized in transporting manpower for exploitation?