Just as a report back, it was (mostly) a success.
Everything seems to be running fine, overall CPU use has dropped dramatically and recordings are now playable again within Kodi.
However...something odd.
My Recordings list has been emptied - both within the tvheadend "Digital Video Recorder | Finished Recordings" view and within Kodi. It looks like they've all been shifted to be under "Digital Video Recorder | Failed Recordings" (that was previously empty). They all have the Status of "time missed", but were all successful "Finished Recordings" before the change.
Only thing I can see in the logs that looks (vaguely) relevant to the version migration is this:
May 26 19:14:42 tv tvheadend[9857]: config: backup: migrating config from 4.1.18~gec3ba93~utopic (running 4.0.1-5~ge776d34)
May 26 19:14:42 tv tvheadend[9857]: config: backup: running, output file /home/hts/.hts/tvheadend/backup/4.1.18~gec3ba93~utopic.tar.bz2
May 26 19:14:42 tv tvheadend[9857]: spawn: Executing "/bin/tar"
May 26 19:14:42 tv tvheadend[9857]: config: loaded
Also, the my upcoming recording timers were deleted (but still exist, so I guess re-created, and not an issue) e.g. :
May 26 19:14:48 tv tvheadend[9857]: dvr: delete entry 97aea402e7f5e04a481b98064707b185 "Have I Got News For You" on "BBC One HD" start time 1432929600, scheduled for recording by "Auto recording by: generic" (duplicate with 40acd7e3b8483fb8db949dec3dab3afc)
May 26 19:14:48 tv tvheadend[9857]: dvr: delete entry c4af5ee3e88a73244c05dd6bbd8fdbdd "Episodes" on "BBC Two HD" start time 1433192400, scheduled for recording by "Auto recording by: generic" (duplicate with f087622c0d8880477ded30f315476b1c)
Dunno if something like what's directly above happens often with an upgrade (or, downgrade, in my case) and I just haven't noticed.
Either way, the missing older recordings isn't an issue for me at all as they still physically exist and I can watch them directly in Kodi under "Videos" through a share (which had been my workaround for the 4.1 recordings not playing directly in Kodi anyway). New recordings seem to turn up fine. Unless, that is, there's a manual way to update these older recordings to be successful as Kodi/tvheadend sees them?