In post about moving to tilde i was thinking about a way to safely merge dotfiles without breaking my tooling that i need to resolve conflicts in case they occur. Well, seems like i found this way. I just cloned my yadm repo locally from ~/.local/share/yadm/repo.git and merged all conflicts there. Then i stashed my changes and pulled the merged version back to the yadm repo.
The only problem left is i may need to resolve stash conflictst as well. Though i think i just shouldn't leave that many uncommitted changes and the problem will disappear.