Where is the Replace/With list stored?
In 10.9 the text replacements are also stored in ~/Library/Dictionaries/CoreDataUbiquitySupport/$USER~*/UserDictionary/local/store/UserDictionary.db. UserDictionary.db is used even if iCloud is disabled and it has precedence over .GlobalPreferences.plist.

If you for example run defaults write -g NSUserDictionaryReplacementItems '({on=1;replace=aa;with=bb;})' and quit and reopen TextEdit, aa is replaced with bb in TextEdit, but the changes are reverted if you open the Text tab of the Keyboard preference pane.

You can change both UserDictionary.db and .GlobalPreferences.plist by using a script like this:

date=$(date +%s)
while read -r replace with; do
  plist+="{on=1;replace=\"$replace\";with=\"$with\";},"
  sql+="INSERT INTO 'ZUSERDICTIONARYENTRY' VALUES($((++i)),1,1,0,0,0,0,$date,NULL,NULL,NULL,NULL,NULL,\"$with\",\"$replace\",NULL);"
done &lt; &lt;(sed 's/\\/\\\\/g;s/"/\\"/g' ~/replacements.txt)
sqlite3 ~/Library/Dictionaries/CoreDataUbiquitySupport/$USER~*/UserDictionary/local/store/UserDictionary.db "delete from ZUSERDICTIONARYENTRY;$sql"
defaults write -g NSUserDictionaryReplacementItems "(${plist%?})"


In 10.8 and earlier versions of OS X the text replacements are stored in the NSUserReplacementItems array (not NSUserDictionaryReplacementItems) in ~/Library/Preferences/.GlobalPreferences.plist.