Isn't it enough to delete the older tweet? Or maybe just add a timestamp to the message.
Off-Topic: If it's not possible to write a twit with the exact text from a deleted twit, then a way to prove someone wrote a twit and then deleted it would be to have them try to write it again.
Deleting tweets is a terrible workaround. Once github start tweeting and people start linking to those tweets they can't go ahead and delete them 50 minutes later..
Re: off-topic:
You have to do it fast. You certainly can tweet a lot of identical tweets if you aren't in a hurry: there is a "Rock in the forest"[1] that tweets "Nothing happened today" (in Russian) every day for several years, and most of the time the text is exactly the same. Interestingly enough, the time of tweet varies widely from day to day, so it looks like a human or a program specifically made to imitate one.
Off-Topic: If it's not possible to write a twit with the exact text from a deleted twit, then a way to prove someone wrote a twit and then deleted it would be to have them try to write it again.