sims.anderson2010

And for the government too! Yes, I did this for the State, but we connected to many fed departments too. There is no "appreication" in this kind of work
If you have not already, look at the last date each of these were opened. My first cut was to take anything that had not been opened for 4 years and simpley put it into a set of DVD's.

Had the HR manager put out a email about cleaning up the old junk an DB to make life better. That each person needed to notify ME personally about any database they had listed in thier job description. Failure to notify ME personally ... not hold me responsible.
Few days later, all DB that had not been opened for 4 years were moved. Burned several DVD's. Wrote an instruction. Sealed in envelope - In your position, the very first thing you do is avoid being blamed by anyone for disruptiong their work.

But, watch your legal side!

Are you a government employee? Or contractor?

I see this is your first post. It is an interesting question. Something I have actually done before. There is a lot of business process involved over and beyond. Are they all MS Access DB? Is SQL Server (that can hold a 100 databases) an option?
Are your databases split (front-end linked to back-end)?

For one small project, I just harvested several thousand Excel templates with data from the network, logged them, opened them (with code) and harvested the data.
I can't put enough emphasis on creating a plan and having it approved by management. The biggest road blocks can be people and process. The technology can be the easy part.
Best of luck