You're 75% there...
I cut the floor in my house remodel in no less than a dozen places and repaired them with no problems.
The fact that you have chipped away part of the flange area, I would just chip (or cut) the rest and then pay a plumber to come in and put a new flange on while you are there. You don't want to have to cut this all up again because the rusted flange broke tightening your commode down.
I musta missed it: Is the piping cast iron? It will take someone familiar with the piping to get the flange set properly. Use a level to make sure you get the flange up enough to accommodate the new floor surface (concrete at level -plus mortar and tile for the flange lip).
If you are convinced the flange is serviceable and level, then proceed with repairs.
Once you get the flange resolved, I'd dig out just under a lip of the foundation (1 or 2 inches below foundation) so the new pour locks in with the existing concrete. Once you get your ducks in line, pour the new concrete. I'd use high strength (5000 psi) on the repair for the extra margin. Have an extra bag on hand in case you run low on material.
I wouldn't try to use concrete as a new "leveling compound" or floor surface because concrete is loaded with aggregate and that ends up not troweling in thin layers. Work the repair in as smooth as you can and then, the next day, pour a $35 bag of Custom leveling compound over the whole floor. Use a 4" chip brush to feather in the edges after you pour. Mix the leveling compound with a drill per instructions and get it poured ASAP. The compound will start to go hot on you five minutes after pour but that's plenty of time to feather in the edges. An hour after you pour it you will be stunned at the quality of the repair you did. It will look like a new floor: Smooth as granite and ready for tile.
If you are tiling, you'll have to resolve the height difference between the hall and the bath floor. Home Depot has aluminum tile edge stripping you can cut and lay in the tile mix across the threshold if needed.
Good luck and good on ya for helping your parents out.
Ray