First, I highly recommend a non-free program I've been using for many years to compare folders/files (both on directory names, dates/times, sizes, etc. as well as comparing on the contents of two versions of files themselves).
The program is named Beyond Compare and you can have it for a 30-day trial, to see if you like it. You can certainly use it on your current problem as a good experiment, to see how you use it to identify the missing 1000 files which seem to have disappeared in your copy process. That's exactly what it does.
Furthermore, it can then "synchronize" between the two sides of the compare, in any of the typical ways you'd like to synchronize. You can simply copy/move from one side to the other, or you can "mirror" so that one side (slave) matches the other (master), or you can do something in between (e.g. copy new and updated from one side to the other, while retaining any "orphans" which are only on the receiving side), etc.
Anyway it's a terrifically powerful but extremely user-friendly and intuitive utility, and I highly recommend it... especially since it's exactly what you're looking for to help you resolve your current dilemma.
Second, as far as ACDSee goes, I have been using ACDSee since back around 1994. I've gone from ACDSee v3 to v4 to v5, and then on to v6 and the assorted "Pro" versions. The last one I bought was Pro v2.5.
I actually do not use any of the more recent and what I feel to be "bloated" versions, as I really only wanted an image viewer/browser that was "lean and mean" and fast and convenient. So to this very day I still use v4.1, and am totally satisfied. I neither need nor use all of the "organizational" and "editing" features purportedly available with these huge newer versions, which unfortunately has also slowed them down as far as just being an image viewer.
Anyway, if you have specific questions on ACDSee I do consider myself to be a master of its image viewing/browsing features so I'd be glad to answer any questions on its basic functionality. However I confess that while I have Pro 2.5 installed, I don't think I've ever used it except to set it up. I like that it can present the detailed EXIF information in digital photos if I want to see the exposure, lens information, etc., but I don't often really need to see that.
Also, if I view NEF raw images from my Nikon camera, I prefer to use the Nikon software and not ACDSee (with its "raw plugin") or even Adobe Photoshop (with it's "raw plugin").
But I'm very experienced with ACDSee in general, so I'll be glad to answer questions if I can.
