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If your clutch is slipping, it could be just adjustment.
First please check the freeplay at the clutch pedal.
Should be easy for first 10mm, check with your finger.
If the pedal is heavy right at the top, it has no freeplay.
Master cylinders either leak at the pedal end, or bypass internally.
Which is what your pedal was doing initially.
Sounds like two things happening here.
You have a noise and low clutch pedal.
They should pull the gearbox out in case the clutch pressure plate bolts are coming undone.
It might not be the master cylinder at fault.
You have a warranty on this from previous job.
The master cylinder could fail after a new clutch is installed, generally from new fluid flushing out the old, and then the cylinder leaks internally.
I have seen that many times, and is understandable.
I am more concerned with this noise that you describe.
If that is coming from the transmission area, then that is their problem to fix.
Did they use genuine flywheel, clutch etc?
Don't agree to the master cylinder until they verify the noise.
Possibly the clutch pressure plate bolts are coming undone.
This will cause noise and slipping clutch.
Hope this helps.