I had some (annoying) error today in my Eclipse instances: Every time I change something in the IDE preferences, the following message appeared and the preferences were rolled back after an restart.

An internal error occurred during: "Store preferences".
Duplicate ID: syncXXX

… where XXX is some integer.

After some googling, I found a non-related bug description that helped me to resolve this issue.

Easily: just remove the file user.setup file in ~/.eclipse/org.eclipse.oomph.setup/setups.

rm ~/.eclipse/org.eclipse.oomph.setup/setups/user.setup

The removed file will be recreated in the next start. You will need to set all the recently changed preferences, but the preferences synchronization will work again.