Do I need to start again every time I use Dispute Buddy?

No. You can change the selected contacts or date range and generate another report in the same session.

If encrypted messages from an earlier session are still on this computer, Dispute Buddy skips How it works. Connect the iPhone to unlock and decrypt the existing index; this is much quicker than indexing it again.

You can then unplug the phone and continue. Choose re-index only when you need newer messages that are not in the existing index. Re-indexing takes about an hour on average, and 2 hours or more for some people.