For files to disappear, your Windows install may be damaged somehow. In over 2 years, no Hoster user has ever reported losing files as you have. If one file goes bad, thats one thing. For all to go bad takes a very bad malfunction in Windows.
We have many users with USB hard drives and I don't recall hearing of a single file being lost.
When was the last time you did a Windows Update? That may shed some light on the problem.
Read this and run DXDIAG and attach the log file to your post here. That will allow us to see your computer setup. Sometimes there is a glaring error that can be fixed easily.
I personally would not try importing more songs until you discover why your Windows is deleting them. Your computer won't be usable in the state it is in currently, and you won't have the confidence to run a show with it that way.