According to Tyler Hicks (one of the maintainers of eCryptfs) it is currently not safe to modify underlying filesystem (lower filesystem in eCryptfs terminology):
It would be good if eCryptfs could detect lower file data changes and update the cache to see the file updated.
Even if we could detect them, how would we mediate them against dirty eCryptfs pages? How do we know what is the most up-to-date data?
Unfortunately, direct modifications to the lower filesystem are simply not supported. If a modification doesn't go through the eCryptfs mount point, we cannot be expected to know about it due to the eCryptfs architecture.