Any other way to fix this than Wrye Mash (which doesnt work for me).

Morrowind has suddenly decided to minimze itself when this comes up so i can't click "yes to all". When i maximize the window it'll just shut down with a "windows is looking for a solution".

Testool:
Use Manage Active Plugins, select all plugins and press "Update Header"

tes3cmd:
tes3cmd header --synchronize *.esp

Great thanks

wrye mash synchonizes this as well. turns the yellow boxes green