I've built two Tamiya ships and don't recall anything like you've described in the kit. I don't think either one of them (USS Enterprise and USS (Ticonderoga) Shangri-La even came with flags.
Sounds like this might just be printed paper that you'd have to glue together, as you've said.
I've made my own flags using white decal stock, finding an illustration of the flag on the web, reducing it to the proper size and printing my own decals. That way, you can recover the lost swastika.
I've had some WWII US Navy ships come with 50-star flags, obviously not right for the time period, so sometimes ya have to make your own.