Hm, I am not sure, but I would prefer to change the sequence of your steps:
First do the import from catalog and accept the missing files in your home catalog.
This should give you the correct flags already, although all files would still be missing.
Afterwards copy your negatives from your card outside LR to your home storage destination.
Then go back into LR and connect the missing folder to the one just created. No import!
With your import you risk that LR is doing something different than your catalog-part.
Personally I would prefer to export also the negatives into your catalog-part, and import everything, rather than doing a second read from the camera card... But that is a matter of taste and should not do anything to or for your flag problem.
Good success, Cornelia
I thought the check boxes would be checkable. I do not have my own test scenario ready, but I read the relevant chapter again in Victoria Bampton's "Missing FAQ", where she certainly assumes that you can check.
But she has checked "Show Preview" in your left lower corner, and can check the individual images in the opening right-hand part of this dialog box.
Maybe this is where you are supposed to check?
(Photos that are identical in both catalogs are dimmed, so non-checkable. Which could not be the case for you)
As a workaround then I'd suggest to include the negatives into your export.
You see I am just not confident that after LR has done its own import it will overwrite its records by the import of a catalog of the same files, which is why I would avoid this first independent import.
Or maybe this is just some *nannying feature*, to drop the reject flags??