This...
the source are APE files that are entire albums as one file, containing all tracks.
and this...
The exact option in the conversion is "Replace original file on disk and in library".
help to explain problem #1.
With all the tracks of the album in one, single file, MC uses the accompanying .cue file to know where each track begins and ends within that one, large file. These are then shown to you as separate tracks that you can play independently of each other, but there is no actual, separate "file" representing these separate tracks that you see. They are virtual references to ranges of duration within that one single ape file, defined in the matching .cue file. All of that is to say, there is no "original file" on disk to replace. This is to be expected and most likely will not be considered a bug. When the conversion is complete and you are happy, manually delete the single file, and the matching .cue file.
The issue with the forward slash could very well be a bug.
I can't be sure as I use Windows, and don't have any "single file + cue file" files to test with. I did try using a single track with a forward slash added to the name, and then again with a back slash instead, and in both cases, the conversion went as expected.