I didn't test but don't you just need to test fileList's length/count before you loop the list…?
onrun
setmyFolderto "/Users/wander5/Desktop/QuarkRescueFolder"
set {TID, text item delimiters} to {text item delimiters, linefeed}
tellapplication "Finder" tosetmyFilestonameoffilesof (POSIX filemyFolderasalias)
setnewNamestoparagraphsof (do shell script "sed 's/\\(.*\\)\\((.*)\\)/\\2 \\1/' <<< " & quoted formof (myFilesastext))
repeatwithifrom 1 tocountmyFiles
tellapplication "System Events" tosetnameof (firstfileoffoldermyFolderwhosenameis (item 1 ofmyFiles)) to (item 1 ofnewNames)
endrepeat
settext item delimiterstoTID
setfileListtolist foldermyFolderwithoutinvisibles
iflengthoffileList> 0 then -- Its not an empty list…
repeatwithtFileinfileList
setrecipientNameto "Wander5"
setrecipientAddressto "Wander5@yahoo.com"
settheSubjectto "Please check Files has been completly copied from server"
settheContentto "check files have been copied"
tellapplication "Mail"
# # Create the message
settheMessagetomakenewoutgoing messagewith properties {subject:theSubject, content:theContent, visible:true}
##Set a recipient
telltheMessage
makenewto recipientwith properties {name:recipientName, address:recipientAddress}
##Send the Message
send
endtell
endtell
endrepeat
endif
endrun