iTunes is referencing the files on the flash drive instead of using local copies. Connect the drive, start iTunes, use File > Library > Organize Library > Consolidate files. If you have media scattered across multiple folders outside the main media folder and don't want to change that then select the files in question, right-click and click consolidate files.
Ideally you would use Edit > Preferences > Advanced > Copy files to media folder when adding to library to prevent such problems in future or drag & drop the files into the Automatically Add to iTunes folder in iTunes Media instead of dropping directly into the iTunes interface.
tt2