repo-updater 3.3 auto-migration: added lots of deleted repos to "repo" list in external service, causing major rate limit consumption

Created by: nicksnyder

See these comments:

• https://sourcegraph.slack.com/archives/GDS3PJ8GK/p1556144436001800?thread_ts=1556144204.001000&cid=GDS3PJ8GK
• https://sourcegraph.slack.com/archives/GDS3PJ8GK/p1556148331007200?thread_ts=1556144204.001000&cid=GDS3PJ8GK

I was able to reproduce this behavior myself by:

1. Running a 3.2 instance of Sourcegraph
2. Connecting a GHE instance with repositories
3. Deleting one of those repositories on GHE (but not Sourcegraph)
4. Upgrading to 3.3.1

@tsenart can you explain why these deleted repositories are kept on the instance? It caused confusion with the customer.

Customers

• https://app.hubspot.com/contacts/2762526/company/561806411