I just tested this on a side database increasing the padding to %07d. Without selecting ‘Change’ all existing Ids received a new leading zero while retaining their existing number.
5.1.5 with SQLite.
The only thing I can think of is that if you did the change from BSDDB to SQLite at the same time you moved up to 5.1. If you did the clean install the defaults for Id formatting would have been %04d with the new gramps.ini file. This might have had an effect on the database conversion.
About once a month I use the tool using the ‘Change’ option selected and the ‘Keep’ option deselected. This reorders my database sequencing after merges and deletes as I continue to document my database. I do not use any custom Id’s.