Yes, that's the problem I see as well. Prep encounter utilities all day long until the final fight. Then switch to daily utilities.It's very powerful to be able to use, for instance, Displacement every encounter until the boss, then swap it in for Stoneskin... so yeah, I'd suggest keeping the partial mitigator.
But is it really a huge problem? There are a lot of ifs and buts with that. The adventuring day needs to be structured like a level of Super Mario. The player needs to be sure that the next fight is the boss fight. Etc, etc.
In theory, this is a significant power-up, but would it really be that huge in practice? I'm tempted to try it out and see what happens.