Walt After looking around some more with Avast it actually has a list of items it will attempt to protect from any changes done to it by unallowed apps.
(As an experiment I turned of picture files and it will now allow any programs to alter pictures, same goes for Cosmoteer, makes sense, as your ship design files are pictures)
You can still allow cosmoteer following the steps I provided above. (once I did that I didn't have to disable any of the shields from Avast)
(Although I did redownload to see if it can work without 'Allowing' your program, sadly I guess it's still a different matter so it didn't work without being allowed)
--In order to fix this, your program has to be more trusted by Avast themselves I guess. since it does say:
(don't really know if you can fix this but good luck! and continue making some good progress!)