Okay found a bug:

If you have files that have the extension .Cbz (with the capital C)

and you use the convert to cbz option it deletes both the original and the newly exported .cbz file.

I stumbled across this when I noticed half the files in a set had mysteriously disappeared upon conversion..and I was able to replicate it.

Confirming this, unsure if it does this on .Cbr's, but I had this happen a couple days ago as well with a couple .Cbz's