This issue seems to be limited to albums which aren’t identified with the program (“scan”, “lookup”). Some of the albums I’m having problems with are my private home recordings and there is no purpose in uploading them.
I’ve only added a folder, then clustered the files and started editing tags. When saving, Picard removes track numbers from the filenames — I’ve reproduced this multiple times. The “track number” tag is saved correctly and created if not in existence.
Tracks on albums with a database entry are renamed correctly.
This is my file-naming syntax (no changes aside from a single dot):
$if2(%albumartist%,%artist%)/$if($ne(%albumartist%,),%album%/,)$if($gt(%totaldiscs%,1),%discnumber%-,)$if($ne(%albumartist%,),$num(%tracknumber%,2). ,)$if(%_multiartist%,%artist% - ,)%title%
Picard version 2.0.3, Windows 10