First, am not a programmer ... just an 'informed' user/server admin with 'seat of the pants experience' who attempts to resolve issues involving Moodle. Sometimes, am nothing more than a sounding board or a provider of thought.
Not sure what is meant by:
'correlation is between my environment, the problem being experienced and your diagnosis post above?'
Diagnosis of a site un-seen, you mean! That's a pretty tall order and I've lost my magic wand ... actually never had one! ;)
Have no first hand knowledge of the CMIS add-on and how that might affects backups - manually or automated. Is the CMIS system used for authentications? That means users are coming from that system and are not really local (to Moodle accounts) ... much like LDAP. In the setup of backups, are users included? Does that mean the backup routine has to communicate with the CMIS system to acquire users to place in backups?
While you've described (very well) your situation, only if someone else has pretty much your exact setup could a more specific answer be provided, thus would suggest other users of the CMIS plugin you've mention get together with the maker of the CMIS plugin to discuss issues/strategies for moving forward (ie, upgrading). If there are many in UK, by all means find out who else uses and inquire if they are having the same issues.
Am almost certain that things like checking logs, turning on debugging etc. will provide clues, but it would be up to someone familiar with the plugin/your system to be able to interpret errors and strategize an approach to fix.
Sorry can't be of more help than that!
'spirit of sharing', Ken