Welcome to TBN! There is no connection between your PTO and the transmission clutch. Your PTO is independent and driven by a completely separate clutch/brake system.
If you shut off the engine, can you shift the transmission? Your problem sounds like a worn clutch that is out of adjustment or a failing thrust bearing/throughout bearing. How much free play do you have on your clutch pedal? You should have 3/4" to 1" free movement before the clutch engages. If you have much more play or much less than this, you need to adjust the clutch.
Also, are there any strange noises when you depress the clutch? Did the clutch work at the beginning of using your flail mower and fail afterwards? Normally, when clutch discs freeze up/stick, it's after a period of inactivity. You should block your clutch pedal down to hold the clutch released when the tractor is not in use to prevent clutch disc freeze-up.