Okay, here it is, a fix to "freezing" flags with imported ships in OH II:
http://www.gamefront.com/files/20738609/Flag_Fix_OHII.7z
I have tested this several times, and haven't seen a single frozen flag yet, but it needs still more testing. Please report any funny business that you encounter with the flags. This fix doesn't affect any other issues in imported ships!
I believe that you can install this without a campaign restart, but I'm not 100 % sure. Best to install in port. Apply with JSGME.
File contains all the imported ships and their files. It's based on latest OH II Full mod.
Trevally, these ships still use the old class system (many merchants are type 104 coastal vessels) so remember to apply your modifications over this.
Happy sailing