The Punchhconf.exe can be re-ran. The executable will look for any updates to the site's configuration and pull down data to fill in the missing store ID.
You can also, although not preferred, copy an aloha.ini file from a different location and replace the store ID. This field is the UNITID which generally is automatically input by Aloha.
If further assistance is required, submit a ticket to Punchh Support. (For help submitting a ticket, click here)