Yes, Final Appraisal does not advance the synthesis step and may indeed break your macro.
However, there is a simple workaround for that. Please create the following ingame macro and put it on your hotbar instead of Final Appraisal:
/ac "Final Appraisal" <wait.2>
/ac "Delicate Synthesis"
Please replace Delicate Synthesis with the action that comes next in your rotation.
This macro will execute two actions at the same step and will advance the synthesis correctly.
Please note that this workaround is not required for Crafting Solver. The solver is fully capable of handling Final Appraisal as intended.