Just add the missing files into the AppGameKit file manually? I have done that in the past and seems to work, only had to because the menu for adding disappeared on me, only add source file was visible! You should be able to right click the .agk file listed in the projects panel and select add file - not add new source but just add file.(this was the missing part of the menu I just referred to).
I have an issue when I open an agk file by association i(e double clicking the agk), but only if it resides in a folder that has been copied(for backup for example or to continue as a newer version). In this situation none of the files show up not even the agk - solved by simply renaming the copied folder anything other than just "- copy" at the end, ie "- copyb" is enough to get it back on track. You could always try that.
I usually also go to C:\Users\usernamehere\AppData\Local\AGKApps and find the same name folder - then delete it because that has messed some stuff up in the past(can't say I recall it being source file related but you never know until you try - BlinkOk did post a proggy in the past for model conversion that used .json files, when BlinkOk updated it I had to delete the .json file from that location before running the new version as it totally messed up the resulting menu options). Admittedly this is a step I often forget to do.
Failing that I dunno, the above was my best attempt of "advice" lol
Win 10 Home 64, Intel(R) Core(TM) i5-10300H, 8GB DDR4, NVidia GeForce GTX 1650 4GB GDDR6
