I will echo: Didn't happen on its own.
Calibre does not tolerate OS level messing below the skirts with filenames or folders.
(that includes direct Adding via the OS) Only Calibre should be used to add/remove/rename books
Calibre was not designed for Multi-access (2+ simultaneous computers)
Active Sync can fight changes. Always pause before running Calibre and
allow it to complete before connecting to another/same Calibre again (your connection may be lots slower than your local drive. Many changes can take TIME to sync)
disable the active A/V scan of the Calibre Library folder (those books were checked when you downloaded them, anyway). That can slow file updates.