Thanks for files. Your files confirm my suspicion as I have 2 other titles, Black Dawn and Memoirs of Geisha, with similar VIDEO_TS.IFO structure that DVDShrink can't open if I remove VIDEO_TS.VOB (114KB). With this removed VOB, I fixed the VIDEO_TS.IFO, and now DVDShrink can open it. I also try FixVTS on the original (VIDEO_TS.VOB only, not the whole DVD) to see what it does, and DVDShrink can open it. I find FixVTS output is not completely clean as my method, and there is a very minor bug, which will be apparent when getting vts sectors on FixVTS output.
So regarding AnyDVD, with "Remove unreferenced and blank cells" checked, I assume it invokes AnyDVD Ripper (equivalent of FixVTS). Based on your AnyDVD files and from what you said, it's correct that the VIDEO_TS.VOB is removed because of the unreferenced vobid, but the VIDEO_TS.IFO info is not updated compared to FixVTS output. As a result, DVD Shrink will give an error. So I would say there's a minor bug in AnyDVD.
This should be very easy fix for SlySoft unless he already knew this and fixed it, then I have wasted my effort. Was going to leave technical details to him in PM but he disallows it. It's understandable. Oh well, he knows what to do.