Jart, the main issue was with the second loop, you need to be looping through every folder of the x folder variable instead. It appears that looping through the folder worked, but when you renamed them it caused an index issue resulting in only reading every 2nd folder.
Here is a little reworking.
- renamed your variables from y and x to be less cryptic.
- changed the length test to support names > 9.
- i was unsure about the item at the end of the new name, and if it should be an incremented number instead. (you can easily revert)
- left in some log calls for your reference, these can help debug stuff
tell application "Finder"
-- Defining Pro Folders
set pro_folder to folder POSIX file "/Users/Jart/Desktop/test"
set all_pro_folders to every folder of pro_folder
-- Iterate through folders and check if folder name is greater than one character
repeat with parent_folder in all_pro_folders
set counter to 0 -- reset a counter variable we use for the end of the name
set child_folders to every folder of parent_folder
repeat with current_folder in child_folders
set fold_name to the name of current_folder
log (fold_name)
if (the length of fold_name < 3) then -- this will allow names > 9
set counter to counter + 1 -- increment the counter every time we find valid folder
set new_name to "Project" & " " & fold_name & "_" & counter
log (new_name)
set the name of current_folder to new_name
end if
end repeat
end repeat
end tell
HTH