I am using antiofflineraid for a offline raid protection and when the base is no longer protected, I want the base to be raidable. How do i make the changes so that true pve is not handling the protection when said base becomes raidable?

if you want some other plugin to handle the protection then you shouldn't use rules that block it
defaultAllowDamage true, and create rules to block damage instead
would be much easier if that plugin used the CanEntityTakeDamage hook provided by TruePVE.

Do you have any advice on what plugin would work well for my needs with TruePVE? Im still a novice when it comes to server ownership and i have been fighting with plugins to get a good online offline setup to work.  I just want peoples bases to be protected while online and while offline have a set timeframe. Once time has expired the base should become raidable, nothing fancy!

Abandoned Base's plugin does this, but it's not free.
otherwise I don't know. you would have to do what I suggested already