Problems with long job. Crashing or losing origin

Cutting tabbed box.
On engrave (50, 97.5 1) engraves well
On cardboard cut (12. 97.5 5) gets 3/4 way (after about 20-30 mins) through then it has error.
Havn’t tried plywood yet.

Thought it might be the usb connections so followed advice to not allow the usb to close down, so went into power management and made sure usb did not close down.

split into two colours half a job for each
each colour will run successfully independently

on changing from one colour to another the system loses origin in that the second colour is displaced in the y axis. Also makes funny noise between colours.

Can run each colour independently, but any suggestions as to how I can run as a single job?

Is there always a problem when running long jobs?

I have had this problem with jobs getting to the high 90% completion before that horrible “rubbabrubbarubba” noise as the axis goes out of alignment. My problem was solved by going back to the stock (short) USB B Cable. I had replaced with a 5 metre long one. I suspect it may be a buffering issue with long jobs and packet corruption on the long cable but I could be talking out of my rectum.

Would that funny noise sound like skipping steppers or slipping belts?