I made the mistake of assigning ships that can't dock to perform a rescue, but now I get a constant load of popup notifications despite deactivating the mod. Any known fix to remove pending popup messages?

Simple change the order for that ship.
On any other.
For example - "Hold position".

And I simple assign it on a wrong ship, and I received only one message.
After that is switched to "Hold Position"

Excuse me. But it is something local. May by some other scripts is interfere ....