Hi Jeff,
I'm not sure how to truncate, but if you right-click the database in SQL Server Management studio, there is a Tasks -> Shrink -> Files option. That might do the trick.
As for deleting Documents, you should never ever delete directly from the DBXL database tables. Doing so could cause catastrophic results. If you open DAT and delete a Document from the Document Catalog view it will clean everything out: all related tables in DBXL plus all tables that you have shredded to.
If you are looking to save space, you can change the "EnableFullTextSearch" configuration option in web.config from "true" to "false". This will break searching from CatBase and a couple other functions, but if you arn't using these (which I don't think you are), then it should be fine.
I'm not sure what you're talking about with querying, deleting, and resubmitting, but I think if you just work from within DAT with delete and/or reshred you should be fine.
I hope this answers your questions!
Matt Faus / Microsoft InfoPath MVPQdabra® Software / Streamline data gathering to turn process into knowledge