Ah ok, this is something I've already tested in a way!
The issue with transcoding doesn't only when transcoding has been running for 1h. It also occurs if the media starts stuttering, I stop it, (+ optionally restart the server/clear temporary files) and then resume.
When I resume and it's ~1hr in, you get exactly the same stuttering. And the number of files at that point can be very low (in the 10s for example) so shouldn't be hitting that limit