In case it should matter to anyone else, a brief summary;
Contacts can be stored on the SIM, on the Phone only or sync'd in the cloud (Google Contacts for me). When a contact is created, it will choose one of those. You can set the default you use, but that doesn't mean everything else will use the same default. Skype for example.
So you may have John Smith with his Skype ID stored on your phone, his cell on the SIM and his email in Google.
An android phone will combine all of those, including combining similar contacts, so when you view your contacts it will not be obvious to you not only which contact is stored where, but how much of each contact is stored where.
If you every combine those [merge duplicates, merge contacts, whatever] You don't know onto which it will centre. You'd think it'd go for the phone default of Google (assuming that you've set it) but not all Apps do that.
So it may be fore you that it centres upon phone only storage. And that is now one contact showing quite normally on your phone but not actually on Google and therefore not actually sync'd and protected.
I used;
contacts / display options / custom / show phone and SIM only
export to CSV
delete all
import from CSV to Google sync'd default on phone.
It takes a few things to come together to cause the problem, but in my case the root cause was Skype's behaviour when syncing contacts with your phone which changes depending on the situation.
Ideally you need to sync your contacts in only one place, and from other Apps that are capable of creating their own contacts be careful about enabling sync.
And ref: comments about backups, I traced the problem back through 1 year of backups and it was still there; all of which were functioning backups but all contained split contact data.
The problem is that in usage it is not easy to detect, and you'd only find out if you lost your phone or it became corrupted.
I hate data issues.
There's gaps int eh story, but it'll give someone else a starting point if they notice the same.
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Contacts Sync new
Contacts Sync new