I always felt like Affleck was too busy with his personal life, and embarrassed by the critical reception of BvS, to want to play Batman anymore. I think he signed up thinking the Snyderverse was going to be much more high-concept than it turned out to be.
There was always the rumor he was contractually obligated to appear in three more movies after BVS, idk if that was true. If it was true, it seems he could have declined to offer his likeness out of a wish to begin distancing himself from a franchise he is officially no longer required to be a part of.
That seems petty to me but actors can be weird about their perception. Especially if they feel recent work has diluted their brand. Affleck was riding pretty high as a director and actor before BVS and, unrelated to the Snyderverse I assume, his recent work just hasn’t generated the buzz he was getting back in the early 2010s.
I’m just thinking out loud though. Who knows, this could 100% be a Hot Toys issue or intentional decision.