Unfortunately you've come across the one big downside of chkdsk - it's actually a pretty dangerous tool when used on a badly damaged drive.
Chkdsk, when run with the
/f flag, has one job - detect file system errors and
attempt to fix them. Chkdsk is not an incredibly smart tool - all it will do is try to fix the errors it finds. This is often at the expense of having to either move data around, or in some cases remove data entirely to achieve its goal. It can occasionally recover corrupt data, but even then it often is only able to perform partial recovery.
Performing chkdsk on a failing drive can also put a lot of extra stress on the drive - it's not particularly uncommon for a drive to be dying and a chkdsk run pushing it over the edge and killing it.
I know it's little use now, but chkdsk in repair mode should never be run on a disk without performing a full backup first for the exact reason you've seen - sometimes the fixes performed can cause harm in other ways.
Tools such as VoidTools' Everything (
voidtools) can search the entire drive to help you find files that may have moved and Recuva (
Download Recuva | Recover deleted files, free!) might be able to restore some lost data, but I'll warn you the chances are slim.
Sorry to say there's very little you can do here if you don't have any backups of your data before chkdsk ran. If the data is absolutely essential, stop using the drive immediately and discuss your situation with a data recovery company.
