First of all, let's simplify your example, removing all the options that are not related to the matter:

find /dir/ \( -name \*dup\* ! -name \*bai\* \) | parallel -N2 "java -jar GenomeAnalysisTK.jar -I {1} -BQSR {2} -o {1.}_recal.bam"

I think that the problem is that there is one "dup" file that does not have a correspondent "dup_recal_report", making parallel switch "{1}" with "{2"}. You should try to print the commands that are executed to a file, and manually inspect them.

Moreover , to remove the the "bai" files, I would use grep:

find /dir/ -iname "*dup*" | grep -v "bai"

Finally, if you know that for each "dup" file there is always a "dup_recal_report" file, I would apply find only to the dup files, and then use {.} to reconstruct the name of foo_1_dup_recal_report:

find /dir/ -iname "*dup*" | grep -v "bai" | grep -v "report" | parallel "echo java -jar GenomeAnalysisTK.jar -I {} -BQSR {.}_recal_report -o {.}_recal.bam"

Model script for solving your problem

step_1: Make a list of type {1} files. ls -1 "Whatever pattern" > list_1 (list all files only of {1})

Script:

for i in $(cat list_1)
do
File_1=$i;
File_2=$('write a sed oneliner to change the name of $i to required correponding {2} file here')
whatever_program $File_1 $File_2 respective command line arguments
done

Your script rocks. This might not be the best approach, but this is what I use often. If you dont follow the script, please comment, I will try to answer your query.