I found a working solution. I post it here, in case others will join this page from Google, one day. Instead of trying to fix the #line issue, I decided to work around those evals. The 'evaled' code is not properly stored in Symbol Tables (much on this can be found also on this site). As the problem is always on the first entering file, I made a wrapper.pl of 2 lines, giving the problem to it, and having my code clean:

 require '/home/jjmoka/TEST/code/test2.pl'
 $DB::single=2;
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This worked both for the simplest example, and for my real production use case (with the proper path in the require).