"look for new and changed media files" rescan issues

For as long as I can remember doing a "look for new and changed media files" rescan produces the following issue:

I have an album ripped as mp3 files scanned into my LMS library. I then rerip the album as flac files and replace the mp3 files with the newly ripped flac files, i.e. I delete the mp3 files and add the flac files, and do a "look for new and changed media files" rescan. What I now get in the LMS library is an album listing showing both the new flac files and the deleted mp3 files. When I try to play the album LMS reports an error since it can no longer find the deleted mp3 files.

A few questions:

1) Has anyone else experienced this issue/problem?

2) Is there any way short of doing a full "clear library and rescan everything" scan to fix this issue/problem?

A related but slightly different issue is that when doing a "look for new and changed media files" rescan LMS will keep rescanning the same changed audio files over and over again with each rescan. In other words, the first time the files are changed, such as renamed and retagged, and a "look for new and changed media files" rescan is done the files are rescanned as changed audio files but then when the next "look for new and changed media files" rescan is done (without doing a full clear library and rescan between the two "look for new and changed media files" rescans) the same files are again listed as changed files and rescanned with each rescan.

And again I ask the same two questions:

1) Has anyone else experienced this issue/problem?

2) Is there any way short of doing a full "clear library and rescan everything" scan to fix this issue/problem?

As I said I believe that these two issues are related and possibly have something to do with how SQLite manages the database.