For the next short while, do not identify any set or unique items in the Chronicle that have dropped from weapon or armor racks. Identifying these items for Chronicle tracking will wipe out data for the entire Chronicle whenever we save out the character next.
You can keep these items unidentified in your inventory or stash right now. Once we deploy a fix during our next server hotfix it will then be safe to identify.
We will update this thread when we have better timing for the Server hotfix that should fix this issue, thanks for your patience.