I did hack similar problem with few steps:
1. Check which of databases has the most files (let's say it is database3 in original example)
2. Put that database first in the command, i.e.

cover database3 database1 database2 ...

it seems to work for me - maybe will help somebody as well.

In reply to Re^3: How To Merge Devel::Cover databases by Anonymous Monk
in thread How To Merge Devel::Cover databases by DrWhy

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