your problem can be more easily solved if you look at this from an another point of view
to obtain that, in printing, page 1 of second pdf file will be not attached to last page of first pdf file on the same sheet of paper, and, more generally, first page of subsequent pdf file will be not printed on the back of the same sheet with the last page of the precedent pdf file
you need to perform a selective addition of one blank page only to pdf files having and odd number of pages
I wrote a simple script named abbblankifneeded that you can put in a file and then copy in /usr/bin or /usr/local/bin
and then invoke in folder where you have your pdf with this syntax
for f in *.pdf; do addblankifneeded $f; done
this script adds a blank page at end to pdf files having an odd number of pages, skipping pdf files having already an even number of pages and then join together all pdf into one
requirements: pdftk, pdfinfo
NOTE: depending from your bash environment, you may need to replace sh interpreter with bash interpreter in the first line of script
#!/bin/sh
#script to add automatically blank page at the end of a pdf documents, if count of their pages is a not a module of 2 and then to join all pdfs into one
#
# made by Dingo
#
# dokupuppylinux.co.cc
#
#http://pastebin.com/u/dingodog (my pastebin toolbox for pdf scripts)
#
filename=$1
altxlarg="`pdfinfo -box $filename| grep MediaBox | cut -d : -f2 | awk '{print $3 FS $4}'`"
echo "%PDF-1.4
%µí®û
3 0 obj
<<
/Length 0
>>
stream
endstream
endobj
4 0 obj
<<
/ProcSet [/PDF ]
/ExtGState <<
/GS1 1 0 R
>>
>>
endobj
5 0 obj
<<
/Type /Halftone
/HalftoneType 1
/HalftoneName (Default)
/Frequency 60
/Angle 45
/SpotFunction /Round
>>
endobj
1 0 obj
<<
/Type /ExtGState
/SA false
/OP false
/HT /Default
>>
endobj
2 0 obj
<<
/Type /Page
/Parent 7 0 R
/Resources 4 0 R
/Contents 3 0 R
>>
endobj
7 0 obj
<<
/Type /Pages
/Kids [2 0 R ]
/Count 1
/MediaBox [0 0 595 841]
>>
endobj
6 0 obj
<<
/Type /Catalog
/Pages 7 0 R
>>
endobj
8 0 obj
<<
/CreationDate (D:20110915222508)
/Producer (libgnomeprint Ver: 2.12.1)
>>
endobj
xref
0 9
0000000000 65535 f
0000000278 00000 n
0000000357 00000 n
0000000017 00000 n
0000000072 00000 n
0000000146 00000 n
0000000535 00000 n
0000000445 00000 n
0000000590 00000 n
trailer
<<
/Size 9
/Root 6 0 R
/Info 8 0 R
>>
startxref
688
%%EOF" | sed -e "s/595 841/$altxlarg/g">blank.pdf
pdftk blank.pdf output fixed.pdf
mv fixed.pdf blank.pdf
pages="`pdftk $filename dump_data | grep NumberOfPages | cut -d : -f2`"
if [ $(( $pages % 2 )) -eq 0 ]
then echo "$filename has already a multiple of 2 pages ($pages ). Script will be skipped for this file" >>report.txt
else
pdftk A=$filename B=blank.pdf cat A B output blankadded.pdf
mv blankadded.pdf $filename
pdffiles=`ls *.pdf | grep -v -e blank.pdf -e joinedtogether.pdf| xargs -n 1`; pdftk $pdffiles cat output joinedtogether.pdf
fi
exit 0