Passengers transfer through Cairo all the time. True, most will be on single, multiple sector, MS tickets; but the transfer officials are used to dealing with cases similar to yours.

There's no question of officials having to find you; you'll remain in limbo-land until they give you the boarding cards and stamp your passport.

But if you have a multi-entry visa, then it might be faster and more straightforward to go landslide and check-in in the regular way. Of course there's no minimum time you need to stay in Egypt.

You'll need to be aware of airlines switching from T1 to the newly (re)opened T2.