You can now just use your old config. Settings will not longer be overwritten and a config gets generates if there is none/you delete it.
New Feature:
You can now "export" your decks to Hearthstone. Not quite sure what to call it. (Button for it is in the top-right in My Decks)
Select a deck in the tracker, click "Export to HS" (it'll tell you to create a new deck in hs and leave the creation screen open) and the tracker will create the selected deck in Hearthstone.
Can be combined very nicely with importing decks from hearthpwn and hearthstats!
This is done purely via mouseclick/keystroke simulations (just like any macro tool), so don't worry, no memory-editing-shenanigans happening.
Does currently not work with golden cards (unless you don't have any non-golden, then yes) because without image recognition there is just no way to do it correctly.
If you/the tracker mess up and is not actually adding in the cards, don't panic and just let it finish.
I tested with all resolitions and it seems to work with all of them.
If it does however not hit the cards/searchbox for you or is too fast: open the config and mess with the values at the bottom. Delays are in milliseconds, the x/y values are percentages. 0.5 means it clicks at 50% of your screen-width.
I could not really test "real" fullscreen, as my hearthstone does not go into "real" fullscreen for some reason.
It restores the window before starting the exporting though, so it should work I think (worst case, if it doesn't, should be a message telling you it can't find the hearthstone window).