You've correctly identified the problem, but I'm afraid that there isn't a simple solution. In fact, it may well be simpler to make the scripts the same in both environments again and rerun the coverage on one of them.

However, if you do wish to pursue the path of matching up the databases, what you would have to do would be to write a program to take one of the databases, copy into it the "Structure" data from the other database, and then munge the run data to either add the missing "use Devel::Cover;" line and budge the rest of the data down a line, or remove the "use Devel::Cover;" line and data and budge the rest of the data up a line.

The API to the database would allow you to do this, I think, but you would be blazing new ground.

If this sounds like a fair amount of rather tricky work to you, then you are not alone. Hence my suggestion in the first paragraph.

Sorry I can't be the bearer of better news.