Open the file with Shpedit
Load an ID flag you
have not changed
Click on SP fix
Note the Old and New numbers will ( should ) look like this
Now go to your modified flag
Change the New numbers
to the same as the old numbers that are shown here and click on Write.
DO NOT manually adjust the X/Y up/down arrows. All you should need to do is change the New "Bottom" -1 to 23 but I have NO IDEA what else you may have tried to do that might change those numbers
All of this presupposes that you built the new ID tag to the EXACT dimensions as the originals