I managed to find out which server was deleting all of the files. So it's a safe assumption that there is a buggy/rogue plugin installed on that server. After some digging, I checked the source of a few of the files, but didn't come up with anything. I then decompiled those same plugins and one of them revealed something interesting.
One of the roleplay plugins I was running was from an older RP mod that I must have forgotten to delete (I switched to a new mod). It's a prop saving plugin, so people can add furniture to their houses, etc. Anyway, after decompiling the plugin using lysis, I found that it contained a couple hundred more lines than the source file.
Here's a pastebin of the source file (.sp):
http://pastebin.com/XJcLshgn
And a pastebin of the lysis output (decompilation):
http://pastebin.com/BB9meNpm
I'm not all that familiar with sourcepawn/c++ but some things still stuck out to me. Specifically, the last 200 lines or so (which were not in the .sp file), starting at line 674 (of the decompiled version, not the source).
Again, I'm not all that familiar with this stuff, so I could very well be mistaken. But it would be greatly appreciated if someone who did know this stuff well could just have a look and let me know what they think.