I’m not too familiar with MHDDFS (I use BTRFS for data protection, replication and snapshots, though ZFS offers similar features), but if it allows for removing old drives from the merge-set, this should work.
Caveats - file ownership, permissions, and final paths should be the same by the time you’re finished. If for some reason you need to change mount points or paths from what they were, you might try this howto on the forum as a starting place for pointing Nextcloud to the new path.
Best of luck to you!