I would start by removing the following nodes (in order, not at the same time)
calculate
smooth
counter
The first 2 store data in an internal array for later computation
In fact, looking at the src of the calculate node, it (for some reason) stores the entire msg object (even though it only appears to use payload in computing the averages!).
It isn't going to be a fundamental config issue, it is what is being done with the data.
You showed an installed node list earlier, but said that some of them are unused. I would start by removing all those that are not used and making sure all the rest are up to date.
You showed earlier you were getting regular modbus timeouts. Do the other systems suffer from this too? It is certainly not impossible that something like this could find a memory leak that has not been noticed previously.
Next time you restart could you show us the full node red startup log please.