You should be able to reimport them:
To get all your missed hands imported
1) Right-Click your Desktop > New > Folder.
2) Go to your \HMArchive folder - To verify the path, go to Options > Configure Auto Import Folders > Edit > Archive Folder: _________.
3) Open that folder and copy the hands (folders of hands) you think it has missed. The archive should be organized by \Month\DayOfMonth (example: D:\HMArchive\2009\07\31). Also get any hand files that are in your \poker site\hand history folder.
4) Paste them into your new desktop folder > HM > Import From Folder.