I'm not too clear on what you're trying to do, but this is what I hear you saying:
You want to maintain a database that a VB program can periodically access and update, that can also be updated and accessed through a web interface.
Using a SQL language, this shouldn't be too much of a problem. Pick a databse that VB has drivers for, and move from there. You'll just have to create interface scripts for it. The VB programmers will have to do the same in their program. IMO, it's not the greatest idea to do a FTP get and parse a tab-delimited file - rather, I'd suggest you just do a SQL connect and perform your transactions that way. It'll be faster, at any rate, and more structured.