Before attempting the conversion, I used this shell script to get status information about each mailbox. It uses 'doveadm mailbox list' to get a list of mailboxes for each user, and 'doveadm mailbox status' to provide summary information. For example (username redacted)
zxxxxxxx: INBOX messages=6 recent=0 unseen=4 vsize=7820215
I used my mailbox status script again after the conversion to report on the maildir mailboxes.
Of the 143 mailboxes found by the script, there are three where the status does not exactly match between the old mailboxes and the new mailboxes. The difference is only in the vsize. Sometimes the new vsize is large; sometimes it is smaller.
I think you did a proper check already. How big are these differences in vsize? Could this not be related to a different way the filesystem is being used?