Oh yeah Cthon certainly can still show up. I saw some speculation that the magical explosion at the end when the temple collapsed was even an intervention from him to keep his chosen one alive so he has a chance to go for another attempt. After all time is of no relevance for a being like him.
Either way it's a perfect set-up to have her show-up somewhere else. Maybe even amnesic and also a good opportunity to introduce Latveria and Dr. Doom while we are at it.