Are you already screwed if you deleted them at the start and plan on replacing them? Both of my maps already have 6-8 hours into them, and I deleted those initial spawns right at the start just like I would've done in Reach and 3.
Just put down at least one new initial and respawn point (forge monitor spawns on respawn points) and you should be fine. If it still messes up though, having someone else join your game and placing a spawn for you should fix it.
The overall rule here: If you have initial spawns, you must have respawn points, and vice versa. I haven’t had any problems on my maps if all spawn points are gone.