P0607 vs Hybrid battery issue

I have a 2006 Prius with 167,000 miles on it. About 2 months ago, I had the dash light up and it was recommended I get a new hybrid battery. Given its age, it made sense. I had it replaced for about $1500. Shortly after, I had the same lights (check engine, red triangle, VSC, etc.) come on. They thought that the computer may need to cycle through and after having the code cleared and driving it, it was fine for a few weeks. The next month, I ended up having my 12v battery die and it was determined that it also needed replacing, so I did. Just a few days later, the lights all came on again. After searching forums, I saw several threads about a leak that often happens, so I checked the back of the car and found about 1/2 inch of water under the spare tire! I had the body shop seal up possible leakage spots where the body connects to the back door, but they couldn't find a specific place it was leaking. A few days later, all the lights came on again.

So, I had it towed to Toyota (not only are lights on, but the battery level on screen is at the very bottom and it does not seem to have any power. They pulled the codes today:
P0A80
P0607
P3000

They recommended I call the battery company (Green Bean) since it's under warranty. However, because of the P0607 code, that company wants me to explore it first. So, Toyota would have to replace the hybrid control module which is estimated at $1000.

In reading other threads, I noticed one about cruise control stopping working intermittently and only resets by powering down. This has been the case with mine for many years, but I don't know if it's connected.

Q: should I replace this module or explore other possible factors? I'm concerned because I know there was water in the back that it could be a contributing factor, but Toyota said there was no water today.

Sorry for the long post!