If the files have been decrypted You should have no problem with the software you have been using.
AnyDVD doesn't "shrink" (compress) it is a decrypter but can be used with other software.
You list DVD Clone do you mean CloneDVD2 ?
If not you should be able to use DVDShrink to compress .
Just to make sure you are working with a DVD compliant folder.
The 6.5 GB size is a VIDEO_TS FOLDER with .IFO , .BUP , & .VOB files inside it?