Thank you for taking the time to report this bug and helping to improve
pdftk.

I get at the moment only
  **** Warning: considering '0000000000 XXXXX n' as a free entry.
from ghostscript with the pdf I tested (maybe related to another bug in 
ghostscript) and
even if I corrupt the xref manually, ghostscript does not fail.

I assume that you do not want to publish/send me the pdf file which finally 
lead to the error
in ghostscript - it would be helpful to track down the bug.

Could you answer some question instead, please?
 - What program/library has produced the origin pdf file?
 - Can you open the split pdf files with a normal pdf viewer? Are there any 
warning messages?
 - There was a "solved" marked bug in ghostscript related to long file/path 
lengths, that led to similar error messages. So, could you just try everything 
in e.g. /tmp/ ?
 - If you run the split pdf files a second time through pdftk (pdftk 
pg_0001.pdf output pg_0001_rerun.pdf), does it fix the error?

Due to different reasons, pdftk 1.44 uses in Debian/Ubuntu again the
bundled itext-paulo library instead of  the libitext-java package, which
were used in the 1.41+dfsg releases of pdftk. This could be the reason,
why it works for you with pdftk 1.41, but not with 1.44.

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https://bugs.launchpad.net/bugs/924039

Title:
  pdftk burst command creates invalid xref entries

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