Use sed to convert the second file into a sed script that edits the first:
sed 's/\([^ ]*\) \(.*\)/s%\1_%\2_%/' file.2 > sed.script
sed -f sed.script file.txt
rm -f sed.script
No loops in the Bash code. Note the _ in the patterns; this is crucial to prevent Sample3 from mapping Sample300 to john.D00.
If, as you should be, you are worried about interrupts and concurrent runs of the script, then (a) use mktemp to generate a file name in place of sed.script, and (b) trap interrupts etc to make sure the script file name is removed:
tmp=$(mktemp "${TMPDIR:-/tmp}/sed.script.XXXXXX")
trap "rm -f $tmp; exit 1" 0 1 2 3 13 15
sed 's/\([^ ]*\) \(.*\)/s%\1_%\2_%/' file.2 > $tmp
sed -f $tmp file.txt
rm -f $tmp
trap 0
