I also had the same experience, but I could only make them restart during the night. So I wrote a monitor to check if any of the Pis lost USB before restarting.
When our business grew, even restarting every night, we would get one or two lost USB warnings every day. One day I didn't receive any warnings. I was really happy, I had fix the issue! Three days later a client calls screaming the service is not working for two whole days and we did nothing. After getting every Pi restarted, I went to check the monitor. Shut down. I asked my business partner about it. "The alarms made me anxious, so I decided to shut down the monitor".
Ah well. Our project was Pis in a crappy mesh network so it lost data occasionally even if they stayed on, and it was not so important to have continous data anyway. We rebooted them every like 3 or 6 hours.
