@OP,
Did the hitch work at all after you had the clutch work?
Did it work and gradually stop working?
Does it work when cold?
Do you have a load on the hitch when trying to lower it?
Does it creep up with the lever in neutral position?
Was there a lot of pressure when you removed the flow control valve or was it only coming out under the weight of the hitch?
Things to check,
Make sure your mechanic installed the vent port on the hydraulic tank/sump and confirm it isn't bocked off. If its good then answer the following.
When you had lowered the hitch and restarted the engine with the lever in the neutral position, does the 3 point hitch hold its position or does it creep up to its maximum upper mechanical limit?
If it creeps up - Check the valve pack that the up/down lever is connected to. I'm thinking that when in the neutral position that control valve is passing.
If it can maintain position in neutral - then I would suspect you got some crap in the flow control valve under the seat and its plugged.
But there's no legitimate reason for it to have screwed up during a clutch job.
Your right although I presume they would have drained the sump at one point to separate the engine from the tranny. Its possible that by emptying the sump they either could have stirred up some crap sitting on the bottom of the sump or inadvertently let something get in the system OR they might have accidentally blocked off the sump vent thus letting the sump build up with pressure as the temperature of the liquid rises and preventing the hitch cylinder from venting to atmospheric pressure.