I'm searching the most effective way of doing the following task, so if someone can either provide a working solution with sed or one totally different but more effective then what I've got so far then please go ahead!

The debugme directory has 3 subdirectorys and each of them has one .txt file with about 48 entrys each.

time (
for FILE1 in `find debugme -name "*.txt"` ;do
    for FILE2 in `cat "$FILE1" | awk '{print $1}' | grep -i '^\([0-9]\+\)$'` ;do
    #for FILE2 in `sed 's/\([0-9]\+\) \([a-zA-Z0-9]\+\)/\1/i' "$FILE"` ;do
        CHECK=`grep "$FILE2" "debug.files"`
        if [ "$CHECK" = "" ]; then
            ## ADD MISSING ENTRY BLABLA
            echo "$FILE2 was missing, added!"
        fi
    done
done
)

Avg result:
real    0m0.174s
user    0m0.052s
sys     0m0.128s

time (
for FILE1 in `find debugme -name "*.txt"` ;do
    FILE2() {
        S=`grep $1 debug.files`
        if [ "$S" = "" ] ; then
            ## ADD MISSING ENTRY BLABLA
            echo "$FILE2 was missing, added!"
        fi
    }
    while read cola colb ; do
        $(FILE2 $cola)
    done < $FILE1
done
)

Avg result:
real    0m0.269s
user    0m0.064s
sys     0m0.228s

[03:53:22] root:~# cat example.txt
52352578 ABF2778ABD^
73534536 LASDM337lA^
83523422 JFAASMM31^

[03:53:25] root:~# cat debug.files
52352578
73534536