Disappearing Tags? Tags as keywords/codes?

Hello. I’m new to DT and already love its potential – but have already entirely messed things up. I spent most of yesterday and last night tagging and grouping about 900 documents (mostly PDFs I created in Acrobat Pro 10). Then at some point I discovered that somehow most of the tags had disappeared from my files.

I had decided I wanted groups for most of the items that I’d organize by hierarchy, but that I would use tags as more of a coding or keyword device. (I used to use Atlasti 6.0, but I switched to DT because Atlas was so time consuming and cumbersome for my purposes).

Then I was reading through the Take Control book/DT manuals about additional functions when I decided to try autoclassify and smart groups and a few other features. Some time later I noticed that most of my files were missing the tags I had assigned to them as keywords/codes. (e.g., I gave items tags by publication, author, year, topic, type of article, themes, etc., and now these have disappeared from most documents, and the items seem to have just one or two tags/groups each.)

I don’t know if one of the steps I tried caused my documents to lose most of their tags. I’ve read through this forum and the manuals and haven’t seen a similar problem. Any help anyone could offer would be greatly appreciated. I use a MacBook Pro, OSX.

Also, is tagging the right way to handle things I want to code for keywords? And why do you see some tags when clicking on a document and others don’t appear except in spotlight?

Thanks so much.