I see the same behavior in Java, reassigning to Local History.
Standard Annotations should not be lost after Local history changes.

the only way i was able to reproduce was when restoring changes via the editable diff view - reassigning

I have no idea why this happens, editor please evaluate.

I think the problem here is that you had the file closed when reverting its changes. Breakpoints in files opened in the
editor are updated when you modify the file (eg. by reverting its changes). Breakpoints in closed files are left at
their original positions, which (depending on the reverted changes) may be moved anywhere in the text (ie. towards the
end of the document if reverting makes the document shorter).

This is definitely not going to be easy to fix, because modules are generally free to grab document positions and
persist them wherever they want and the editor infrastructure has no way of telling the modules that they have to update
them. There could be even bigger problem in the general inability to detect external changes made to files.

This will be resolved LATER.

NetBeans.org Migration: changing resolution from LATER to WONTFIX