Everytime I run emaint I see this and it get's never fixed. Emaint: fix cleanresume 100% [============================================>] 'app-arch/lbzip2-2.3' does not exist in the portage tree. 'sys-kernel/lh-sources-3.12.4' does not exist in the portage tree.
This message appears to come from MergesHandler (emaint's "merges" module), and it seems to be incapable of fixing this case. The message should go away if you manually remove the corresponding -MERGING- directories in /var/db/pkg.