Falling out of the bunk bed and damaging the floor.

Did I read the first post right? Are we talking 4" deep or 1/4" deep?

If it is 4", you can.t use a filler because there is nothing to support it. If you use a self leveling filler, it may set up, but there is nothing to hold it up once the subfloor is gone. As soon as you step on it, it will let loose.

You have to get to the supporting joists under the floor and replace enough wood to get back to those. This could be very hard just from the top- hard without making a mess anyway.

Good Luck. Charles