Since the removal of the extra damage/armor upgrades, the system still acknowledges the missing nodes. It's a bug that you'll just have to deal with until it's patched, but you're not losing any upgrades or xp.
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Edited by Dub Graves: 6/20/2015 8:29:18 PMAhhh that makes a ton of sense. I didn't think it was a problem, it was just something I noticed and thought was a little strange. Thank you!