Calibre removing books when connecting devices

[Rika24]

i mainly use my Nook HD but decided that i wanted to update some of the old fanfics with new chapters on my Sony touch edition since i haven't used my it in a while, but when i plugged it in and opened calibre my library was a mess.

if the book wasn't on the sony it disappeared from the library entirely (including the folder in my user directory) and for the stories already on the reader, it replaced all the newer fanfics in the library with the older ones that were on the sony.

i've got everything set back up again (thankfully i had a backup on a flashdrive) but i wanted to know if there was anything i could do so that this doesn't happen again (i haven't reconnected my Sony since this happened). i would like to be able to use both readers without having to redo my library every time.

i connect my nook HD to calibre through wireless since i can't connect directly on my Mac (not sure if that matters though).