HELP entire files disappearing from folders

[Sakusha]

I'm working on one of my final projects for school, I created a folder in Pictures via Finder to place my WIPs (work in progress) The program I'm using is Manga Studio which writes files as .lip, so for example in my folder I have Page 1 WIP, Page 2 WIP, etc. Then I started to notice entire files (Page 3 WIP for example) are MISSING from that folder even though I clearly remember and re-saved that file into the folder.

I did an experiment where I created a folder on desktop and named it Test, then I proceeded to place files from Manga Studio into that folder on the desktop labelling these files in order (Page 1, Page 2, Page 3, Page 4, etc.) up to Page 7. For some reason only half of the files are showing up in the test folder (Page 4, is missing, Page 6 is missing).

Is there a solution to fixing this? I don't want to keep working on my project if entire files keep disappearing from my WIP folder.

I'm on OS X Yosemite 10.10.2

 

[PsyOpWarlord]

Have you done a search on your user folder for .lip to see if they are somewhere else on your drive? Depending on where they are going might give some insight onto why.