Ascension ----> Regional League

If a team such as Apeks in EMEA goes up to the league and they were able to qualify to master and place consistently through the two year's can Riot decide to keep them in the League?

Probably not

They will be relegated after 2 years

remember franchising is about the orgs not the players so they wouldn't
In that scenario they would likely just get poached when the org goes back to tier 2

unless the org provides some immense value where adding them indefinitely helps riot i cant see them keeping it, if that org goes on in the first 2 years and wins something and has a huge fan base around it riot could always extend a contract but most likely the players will get poached with maybe a few that don’t get offers.

It could only happen if one of the orgs in franchise decides to pull out of it.