I have learned a few things throughout the unfolding of this thread, out of which the most important one seems to be:
If it ever comes to amending a reference, don't do it on your own, instead first involve your own employer and ask for their guidance on this. See more in @gnasher729's answer and @CCTO's answer.
As a reference, you had one job.
Now, will you fulfill that job, or will you abandon it while half done, in a misleading state?
See, that's the problem. Now the ball is in your court. It's about whether you can fulfill an official role responsibly (which in turn involves your reliability, and thus, reputation).
What had your colleague's choices been?
- Your colleague could have done his prank — but not ask anyone to vouch for him beforehand.
- Or he could have asked those vouching for him up front about how they would feel about a little prank on the last day.
- Or he could have opted out of doing his prank.
Your colleague had a generous amount of room to maneuver.
Yet he chose a path that:
- caused damage to your workplace
- caused difficulties to your entire department
- and had set you up in a difficult moral situation (as follows).
What are your choices?
- either look the other way, on grounds of camaraderie, but let the other people at the new workplace down (with whom you had already been in an official exchange regarding this person's conduct),
give a phonecall to the new employer get the guidance of your employer on how to amend your recommendation, on grounds of responsibility and credibility.
You seem to be stuck between a rock and a hard place.
However, if you let this slip:
- you will have to walk around every day never knowing when the person — enjoying trust your word had lent him — does his next ill-concieved "joke",
- you can't know if / when does the new workplace find out about the prank at your workplace and that you had remained silent,
- if they find out about it, you will get labelled as untrustworthy beyond repair,
- plus you need to consider how you will feel, all this while.
What you might also want to consider:
A "prankster" "pranking" a company might rarely be in total control of the extent of the damage that their actions are causing. It's hard to carry out anything like that without risking any further, unforeseen collateral damage. Can you be sure that a next "prank" will not, in some unforeseen way, endanger someone? When you — as an official reference to a person — remain silent about such an issue, you become an accomplice in such reckless, risky acts happening — at least as long as the person works at the company you had given your reassurance to.