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Two instances migrate the same version 1 file (useShiftKeyForToolSwitch false -> true), so both save bases hold false. When B turns the switch off and saves version 2, A's next unrelated save wrote its migrated true over that choice. write_prefs now drops the migration delta from the base when the file on disk is already version 2 or later. Test: another_instances_shift_tool_switch_choice_beats_this_ones_migration (fails without the fix: true written over false). Co-authored-by: Higgs32584 <55243596+Higgs32584@users.noreply.github.com> Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>