The current translation-tool.pl that is available at https://github.com/jenkinsci/jenkins has the option --remove to remove orphan keys from the properties files (for example, there are keys in pt_BR files that doesn't exist in the original English ones).

When the tool is executed with the option, the report is not updated after the remove is done (i.e., the files are already updated). It is necessary to execute a second time to get the actual number of keys that are still orphan (hopefully, zero).

Here is an example:

TOTAL: Files: 663 Keys: 2062 Done: 1245(60.38%)
 Missing: 712(34.53%) Orphan: 82(3.98%) Empty: 5(0.24%) Same: 18(0.87%) NoJenkins: 0(0.00%)
$ git status | grep -c modified
41

Then a new execution, but without any modifying option:

TOTAL: Files: 663 Keys: 2062 Done: 1314(63.72%)
       Missing: 719(34.87%) Orphan: 9(0.44%) Empty: 2(0.10%) Same: 18(0.87%) NoJenkins: 0(0.00%)

Not sure why there are still 9 orphans, need to investigate further though.