Looks like you got it - this seems to be exactly the problem:
The scanner resets all LCNs to zero when the LCN Finder is set up, then replaces the zeros with the ones it established.
In most cases, I am exiting after finding
some of the LCNs. For example, one of the systems has 5 frequencies, but only 2 or 3 are actively busy, and unless I leave it there for hours, I only get 2/5. When I exit, I am exiting with 2/5, or 1/3, etc, and I am prompted to save the LCNs, which I select yes. When the LCN finder indicates that it has found, say, 1/3 LCNs, 1 LCN does indeed show (or however many it has indicated as found), and the rest are 0, so that explains it. The other frequencies are definitely part of the system, but I only leave the LCN finder on for 1-3 minutes, just to verify a few of them, and I had no idea it would delete the ones that I already had verified.
With that figured out - that is a pretty stupid implementation of the tool. In most cases, I already have most of the LCNs, and just want to either find or verify
some of them. I figured that it would just add to the existing information, or edit any wrong entries.
I know I could simply take the information the LCN finder has saved, and then manually re-enter the ones that were reset, but that pretty much ruins the whole point of the tool, for me at least since I then have to repeat the process of read/write another time, which means more downtime. It would be easier to use DSDPlus only then, and verify/edit anything missing/wrong.
I guess I will just stick to DSDPlus for LCNs for now, unless I am on the road and dont have access to my computer. In that case, I would probably be better off deleting the less-used frequencies, or risk waiting an hour or more for the whole thing to complete.
Hopefully Uniden sees this and at least makes an option not to reset all the LCNs when using this tool. It would be a lot more useful for people that are just trying to verify certain frequencies on the system they are monitoring.
Thank you for the explanation, I would have been going in circles thinking I had an SD card formatting error or something.