I have been experimenting further with this issue.
I opened a new test server with full default PVE settings and changed the decay settings to those I am using on the Siptah + Exiled Server. At first, it was still having the same problem. So I set it to default again and changed the values one by one with a reset in between each change.
Ie.
Increase Structure Decay Time > Restart Server > Decrease Auto-Demolish Time > Restart Server.
This solved it for the test server. Repeated the same steps with the Siptah + Exiled. Still not working.
Observation 2:
So if I go to a base, it will display the decay as 504h (3 weeks). If I leave and return 3 hours later for example, it would display as 501h, which it should do. But after a server restart, if I go back to that same build, it will be back up to the full 504h.
But after checking the event log, some structures from parts of the map we have not been to in a long time, have actually decayed.
So for a more accurate description of the issue at hand -
After a server restart, if a player visits a structures not owned by them or their clan, it will reset the decay timer to full. The Decay timer will then countdown as normal, until the next server restart, in which the issue repeats.
If there’s any mods/devs that can drop a reply so I know the issue raised has been made aware, that would be hugely appreciated 
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