Upstream has released updates that appears to apply and compile correctly.
This update has not been tested by PaperMC and as with ANY update, please do your own testing
CraftBukkit Changes:
fc10dec5 Don't throw error on invalid data in CraftMetaItem.
Fixes GH-1471, GH-1474
As a result, data that no longer parses correctly will not crash the server
instead just logging the exception and continuing (and in most cases should
fix the data)
Player data is fixed pretty much immediately but some block data (like
Shulkers) may need to be modified in-game in order for it to re-save
properly
No more crashing though.