Are these engines Proto 2 or 3 that are having issues ? Are there working engines with no issues on the layout ?
Do you ever get the problem ones to power up with the remote ? If so. Are you deleting them and re adding them ? Or are you moving them to another piece of track ?
A piece of track with a bad signal can cause issues as well as a weak battery in the engine that will cause it to lose it’s memory. This can occur in a Proto 2. They can always be deleted and re added. But after sitting overnight. You have to go through the same sequence again.