Ok so, regarding the flags of the Gran Colombia region, they would look fairly similar to OTL. Now, with Perú and Bolivia, iirc we had them become one upon independence instead of uniting later on. This would mean that the flag wouldn't necessarily look like OTL flags. The first national flag of Peru was created by Argentinian libertador José de San Martín, but he couldn't be part of the liberation given how Argentina doesn't exist. So I would try to just make up a flag using Inca symbology (as this Gran Perú would take a lot of inspiration from the Incas).
I must have forgotten about the plan for Peru-Bolivia. I thought it formed like IOTL, but this sounds good as well. In that case, Inti will feature on it for sure, it might want to avoid the rainbow flag because its a little messy and might be a little too funny to folks from OTL to see a country with the gay flag. It also doesn't really fit with western vexillological practices at the time and is likely a modern invention anyway. I think that the flag will be a tricolor or some other modern European division of field with Inti placed on it. The only other thing that might be expected is that red will be present, because revolutionaries love that blood symbolism on their flags. IMO, the flag I had up there but with Inti on it could work just as well as any other flag, but if you can think of anything else that is particularly fitting. Maybe blue might be included if Miller's flag still exists, but I don't know about that.
Also, was the pre-Bolivarian blue and white flag of Ecuador based on anything Argentine? It looks like it was, but I can't find any sources indicating that.
Also remember that Bolivia probably isn't named like that. Alternatively, you could have the Peruvian flag take some inspiration from the Colombian flag as Bolivar would be the main man behind Peruvian independence, but not too much as Peru would become a rival to Colombia.
Regarding the Platinean countries, I haven't actually thought about flags so far, but I will probably will have to make some flags up as there was no regional symbolism that I know of in La Plata.
Yes, in terms of the naming, I think that the whole country would initially be called Peru (retroactively referred to as Gran Peru), with the states maybe being named after the Incan Sulus given the focus on Inca imagery and a desire to distance themselves from Spanish colonial influence a bit to assert their independence. So *North Peru would be Chinchasuyu, *South Peru would be Cuntisuyu, *Acre/Amazonas would be Antisuyu, and *Bolivia would be Collasuyu and then choose a different name after independence.
As for La Plata, I'm sure you'll come up with something good.
I realize now that we never decided on a flag for the UKCA either. Damn.