Actually, thank you so much for mentioning this! It's not a Lua thing, but a save file thing. In order to keep track of which themes are for which projects a save file stores the location of each projects and files (it's in Appdata/Roaming). I have a feeling it was probably seeing the original location, saving it, and then having those issues.
I am so glad it's working for you now though. That makes me happy! If there are any other issues, please let me know. I'm going to make it so that in future updates (one coming before the end of this month) it will use relative directory names for the themes and the save file, rather than hard coded. That should keep that from happening again (finger's crossed!), in case anyone else has the same issue.
Thank you for letting me know that's what fixed it for you. I was worried! I was hoping we could find a solution, and glad one came out.