repair of bad floor

It's very labor intensive to repair this time of damage. So it depends on your income, free time and skill level. You need to find the leak(s) stop them, remove and replace all damaged wood and what you need to remove depends on how extensive the damage is.
I've done this type of repair twice and vowed to never again, good luck, I fear you will need it.

Sorry, Wish I could give a better answer, but without seeing picture or very detailed description; sort like talking the dentist over phone. Does it need filled, pulled or capped?

By the time some users have ignored the spongy floor over time, it may be necessary to replace some of the floor framing, also.

I removed all the plywood, replaced some joists, insulated the spaces, drilled new plumbing through holes, and installed new plywood in my old TT. Totalled about 15 hours. I did have the advantage that all the cabinetry and trim was removed at the time.