I know this is an older post, but I found it, and found some useful information in it, so I wanted to add what I was able to do to fix the issue - though it is fixed with a bit of a club, not a scalpel.
-- Summary:
-- Regex find.
(trackingBodyName = The Sun([^\r\n]*\R+){17})(^.+?actionGroup = )(None.*\r\n)
--- regex replace.
\1\3Custom10\r\n
In essence, yes, Kopernicus is the problem. One element of the MOD is upgraded solar Panels. Any Panel that can track the sun - and that's all extendable panels - are updated. But my those rings of Jool are nice arn't they? Well worth this pain, right?
Anyway, during the update it strips out the action group items. From day 1 I had configured all extendable solar panels, along with Antenna and anything else that was essential for Craft startup, or could burn off during re-entry, to use the Zero key, or as KSP knows it "Custom10".
Kopernicus edits the persistent.sfs, and adds the XML tag "trackingBodyName = The Sun" to each every extendable panel in the file. 17 lines down from this tag are the action group elements. Changing the ExtendPanelsAction element, actionGroup tag, from "None" to "Custom10" will allow said solar array to toggle with the Zero key. It does not affect any other already-assigned items, such as Antenna.
I had 642 trackingBodyName tags, and some were already configured to Custom10, as I launched ships before I realized what I was dealing with, and how extensive the problem was. So I only had 631 solar panels, across all my active ships, stations, probes & rovers, that needed to be updated. Obviously I wasn't doing THAT by hand. So, I developed the following regex expressions to do the find and replace fore me.
Steps to resolve.
1) Save the game and exit out.
2) Create a backup copy of your persistant.sfs file.
3) Open the persistent.sfs file in Notepad++ (It is free to download off the web if you don't already have it.)
4) Do a find. (CTRL-H) and hit the radio button for "Regular Expression" at the bottom of the find window.
5) Drop in this FIND regex string...
(trackingBodyName = The Sun([^\r\n]*\R+){17})(^.+?actionGroup = )(None.*\r\n)
6) OPTIONAL do a count so you have an idea of how many solar panels you are about to update.
7) Click the "Replace tab"
8) Drop in the following REPLACE regex string....
\1\3Custom10\r\n
9) Replace all.
10) Save the file,. Launch your game, and load your save. (NOTE: If you have had this issue for a while, and go back to an old quick save, or other save, you will loose all the changes. You can do the same edit to all of the save files.)
This resolved my issue - at least, for the way I use the solar array action groups. (On one class of ship, one that has 8 child probes, and where I had each prob set to use an action group to prep it for flight; I.e. probes numbered 1 - 8 were on action groups 1-8. Now, all of the probes solar panels are tied to action group 0. This is the "Club" part of the fix I mentioned above.)
Hope this helps. and good luck.
InCrypt_