ipad/icloud keeps deleting PDF files but I can't find them in recently deleted

I have been struggling with keeping my PDF files on my ipad without them mysteriously disappearing. They are annotated articles that have all my notes and everything for school, and they keep getting deleted but I can't find them anywhere. I'll be working on it one night, and then the next morning I can't find the file or it won't let me open it, saying it "doesn't exist". I have tried saving it to my iCloud and directly to my iPad but it keeps happening. I don't think it is a storage issue either because I have plenty of storage on my iCloud and iPad.