I use a smart rule to fix these types of emails:
Script:
on performSmartRule(theRecords)
tell application id "DNtp"
--set theRecords to (get selection)
set n to (count of theRecords)
set theCounter to 1
show progress indicator "Converting EMLs…" steps n with cancel button
repeat with theRecord in theRecords
step progress indicator "(" & theCounter & " of " & n & "): " & (name of theRecord)
set thePath to path of theRecord
do shell script "/usr/local/bin/dos2unix " & quoted form of thePath
set theCounter to theCounter + 1
if cancelled progress then exit repeat
end repeat
hide progress indicator
end tell
end performSmartRule