upgraded USB, getting read-only errors

I just upgrade my OMV install media from an 8GB flash drive to a 32GB flash drive because I was down to like 5% disk space and couldn't run updates anymore. I used Clonezilla to clone the drives, then Gparted to grow the partition on the 32GB drive. But when I ran 'apt-get upgrade' via SSH I received the following message and nothing else happened. I'm running Erasmus 3.0.92. No matter what I do I get these "read-only file system" messages. And, my services (e.g., Sonarr) are taking ages to load. It took about 5 minutes for Sonarr to load, then another 5 min or so to navigate to do a backup because it each page was loading so slowly. How can I fix this?

Traceback (most recent call last):
File "/usr/sbin/omv-mkaptidx", line 68, in <module>
cache = apt.cache.Cache()
File "/usr/lib/python3/dist-packages/apt/cache.py", line 107, in __init__
self.open(progress)
File "/usr/lib/python3/dist-packages/apt/cache.py", line 154, in open
self._cache = apt_pkg.Cache(progress)
SystemError: E:Problem syncing the file - sync (5: Input/output error), E:Write error - write (30: Read-only file system), E:IO Error saving source cache, E:Problem renaming the file /var/cache/apt/srcpkgcache.bin.cRK80r to /var/cache/apt/srcpkgcache.bin - rename (30: Read-only file system), E:Failed to truncate file - ftruncate (30: Read-only file system), E:Problem renaming the file /var/cache/apt/pkgcache.bin.9XCZdN to /var/cache/apt/pkgcache.bin - rename (30: Read-only file system), E:The package lists or status file could not be parsed or opened.
W: Not using locking for read only lock file /var/lib/dpkg/lock
E: Unable to write to /var/cache/apt/
E: The package lists or status file could not be parsed or opened.

Also, I noticed 'python3' is eating up my system resources:
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
8618 root 20 0 2283636 2.069g 14100 R 100.0 54.2 16:29.25 python3

First, can I check it without deleting everything on the drive and re-doing all of this work? I bought this drive from my employer's IT dept. They're supposed to test all hard drives, flash drives and memory before we take possession. I buy most my flash drives from them to avoid losing money on potentially counterfeit devices.

Second, I plugged in my old flash drive and noticed it wouldn't boot into OMV without an fsck. It's a drive I had in this system for 4 years or so before finally upgrading it. I think done a block-by-block clone I might have copied these issues over. Is that possible?

I shut down the machine. Booted to a prompt then ran fsck to check and repair the system. Seemed to return a lot of the errors I had when I tossed the 8GB USB drive back in. Now things more or less to be working. I've spent several hours updating the system. It's actually working now. But Sonarr and Radarr don't load quickly. My other services are running fine but these two aren't. It takes forever for either to load the web interface. I'll see if this is corrected after the updates finish and I reboot the system. At least I can write the drive properly now.