I have read about this on different places aswell on this forum.
I would like to mention that I too have similar effects from my ide and board manager. What I have noticed is when I disconnect from the internet but still work via my wifi router thereafter not only does the 8266 boards disappear but also any other boards that was loaded via the manager for example the attiny 25/45/85 boards. I can work for days without any problems if I stay away from the router. It would appear board manager tries to check for updates and being unable to connect via the internet then aborts and those files disappear. With the next connection to internet the files are restored. But without a refresh from the internet all added boards are unavailable. This operation does not seem to happen when working iso ie not with router connected. Does board manager only check for updates when it sees a connection to the internet? It is rather anoying when I would want to test a connection to a 8266 via the router just to find that next boot or board change only to find the bear ide available without the added installed boards via the manager. I have more than one board in the prefered list.