Can't be much help but frankly I have
never seen JRiver remove a file unless I manually tell it to delete it. Most files that disappear I find are really only gone from the library and never removed physically from the hard drives.
I don't see how changing your configuration would have anything to do with file deletion, unless you have some autoimport rules have some fancy replacing expressions in them. I avoid anything automatic in import except maybe building thumbnails, but I do like that it fixes broken links. I never have JRiver move anything automatically based on conditions (do you? Myabe they are not erased they are just moved somewhere else, I know that's a long shot
)
Its funny though because I've read people saying that it is better to set fix broken links to no before. The only reason maybe would be for having USB external drives that don't have fixed drive letters (?) which I really avoid and only use for my second archive backups. Maybe its different on Macs or Linux. Personally, I think the best all around config is to set
Fix Broken Links to Yes: Protect Files on Missing Drives.
Update for external changes I need/want to be on as sometimes I use external tools on files. What I think should
not be checked is "
Ignore Files previously removed from Library" which I find problematic sometimes. Easy enough to remove items, not always easy to find what might have been omitted. IMHO of course
Regardless, unless there is some automatic stuff going on that goes beyond basic configuration, I don't see how these options would get rid of your files.
Maybe check your RAID configuration (again a long shot so probably not).