If you backup the DB and disable The Dude on that router, does the cpu stays at 100%? I would try removing The Dude and running the CCR without it for a couple of days and see how it behaves. Then import the DB and see how it behaves. If you have a spare CCR try putting the backed up DB into that CCR and check how it behaves.I have the same problem with v6.46.5. Dude server on CCR1016-12G.
Starting with version 6.46.4, I have to disconnect the server since it starts sending a large number of requests. The kernel load rises to 100% and leads to a freeze in the winbox service (maybe not only it). I expected that in 6.46.5 the problem will be resolved, but nothing has changed
Clearing and compressing the database has not changed anything. Turning off monitoring for half of the devices also did not change anything.
There are 1,132 devices in total.