Regarding folder structure (by the way, no one cancelled the 260 character limit, which, for example, still exists in Windows7) I agree with what
vimmers says. The shorter the path leading to the game folder, the better. In Windows 10 build 14352 this NTFS file system restriction (260 ch.limit) has been removed, but the user needs to change the security policy to activate it--> gpedit.msc, go to Local Computer Policy > Computer Configuration > Administrative Templates > System > Filesystem > NTFS, and set Enable NTFS long paths to Enabled.
Anyway, I'm glad (if I understood you correctly) that your problem with loading the save file from ep1 to ep2 has been successfully solved after downloading ep2 from another source. As for the error analysis and the peculiarities of the in-game code, I can only advise you to try to write in pm to
Ragnaroekr who is a member of the team and the closest assistant of the game developer. If he has the time, he will be able to give a more qualified answer than I did.