But many lines in of the file "finalidlist" that consists of PubMed IDs is skipped. Can anyone help me whats the problem?

Maybe the problem is not in the code but is in the finalidlist file which you haven't posted. If your example isn't self-contained then it cannot be tested. See SSCCE.

In the meantime:

• You have not used strict
• You have not used warnings (it's there, but you've commented it out!)
• Your indentation is inconsistent
• You have used XML::Simple (despite the warnings in the documentation not to) but have not then subsequently referred to it in the remainder of the code
• You do not test the result of your HTTP request operation - what happens if it fails?
• You do not test the result of any of your open statements - what happens if they fail?

See the Basic debugging checklist for why these things matter.