This issue is not caused by a known bug or limitation rather (#177073) because it is a result of how the Schedule works. The Annotations are thrown away when the Criteria set changes and an element is not listed anymore. The workaround could be annotating at the end of the design process and saving multiple Schedules instead of changing the View settings of them (changing the Schedule's View settings could also cause the same symptoms).
Archicad 4.55 - 24 | HP Z800 | Dual Xeon X5667 | 48 GB RAM | Nvidia Quadro P1000 @ Windows 10 Pro x64
Technical Support Engineer