The borg seem to not be able to adapt to everything at once which is why holodeck bullets worked that one time and phasers initially work, so presumably between encounters with starfleet they fight other things that force them to adapt away from resistance to starfleet weaponry and starfleet in kind change their phaser frequencies so the borg can’t just re-implement the resistance they gained last time.
The borg seem to not be able to adapt to everything at once which is why holodeck bullets worked that one time and phasers initially work, so presumably between encounters with starfleet they fight other things that force them to adapt away from resistance to starfleet weaponry and starfleet in kind change their phaser frequencies so the borg can’t just re-implement the resistance they gained last time.