Using 3.5.8233 P, this appears to be a regression as it does not happen with 3.4 - and, for me at least, is repeatable.
Basically I drop a folder containing a single FLAC rip and its CUE file into the inbox, select the album and convert it to MP3 (320, using "replace the source file" setting) and MB correctly produces the individual files as expected (in the folder).
However, when the conversion is complete the album simply vanishes from the inbox, and must be "re-dropped" for the usual tag editing. And by "vanishes" I mean the files remain where they are supposed to be on the disc, it's just that the album is visually wiped from the inbox, and attempts to F5-refresh have no effect.
This only happens with single FLAC + CUE conversions... if the album is already in separate FLAC files, the album display remains as expected afterwards.
Also, (unrelated to the above), folders which have a '.' anywhere in the name ("Jarrett - Köln (44.1kHz)" can't be dragged into the inbox (the cursor changes to "blocked"); however, editing the name to remove or change the '.' character to something else such as "44-1kHz" will allow dropping as usual. Strange.