Option 1 (Quick fix): Run SQL to remove the missing model references:
DELETE FROM ir_model WHERE model = 'some.model';

DELETE FROM ir_model_fields WHERE model = 'some.model';

DELETE FROM ir_act_window WHERE res_model = 'some.model';

DELETE FROM ir_ui_view WHERE model = 'some.model';

Option 2 (Best practice): Use a separate database for each branch to avoid model conflicts.

Option 3: Switch back to branch A, uninstall the module, then switch to branch B.