You have an Operator Presence Relay that is powered through the seat switch to complete the ground circuit of the PTO.
A bad connection/switch at the seat switch, OPR or PTO connection could be the culprit.

For starters-
Before the problem occurs try this-
With the key ON (not running) engage the PTO switch.
Manipulate the seat switch.
You should be able to hear the PTO and OPR click.
When the problem occurs, do the same thing and see if the OPR is clicking.
IF NOT, the OPR is bad or has a bad connection.

Another possibility is that you are shifting around in the seat after mowing awhile and a marginally adjusted Seat Switch is disengaging.

You can go into more extensive PTO tests, such as jumping 12V and ground directly to the PTO to see if it engages.