What do you mean by
when I restart the run it starts just fine until it clears
If you feedhold and then that stops your machining process entirely.
If you feedhold the machine for a period of time and hit cycle start again, what exactly happens?
I don't think I've ever had an issue like this.
I have jobs that will wait on toolchanges over night and I come in the next day and change the tool with no issues.
I've hit feedhold on a machine before and went to help other people in the shop to come back and hit cycle start again with no issues.