PS: Is there maybe a limit on the size of the .vis file or on the number of scenes/objects/variables?
Nope. One of Daedalic's upcoming games is massive with well over 100 scenes apparently & a load of characters, objects & so on. As I've already mentioned; it's likely you've done something recently (by accident) that is causing the issue. Loose way point in the way borders of a scene, overlapping way border line or a way border line is too close to another one. Added a none recommended audio or image format file somewhere. Added some Lua script that's causing an error. Something...
Quick question #1: does it play ok when launched from the Visionaire Studio editor?
Quick question #2: how are you exporting the game? everything inside of main vis file? some things in main vis file? each export type into a single container per type or as individual files?
Quick question #3: are you working on a windows machine, a mac or both? is the export for windows? for mac? are you exporting windows build on a windows machine & the mac build on a mac machine?
P.S: if you want, feel free to zip/rar/7zip up your ved & resource files & send them to me. I would probably be able to figure out what the issue is a lot faster if I take a look myself. Otherwise without that or screenshots it's all speculation on my part.