The Smart Client Packager does not retain changes made to the shortcut name.
The default to the shortcut name is "APM Client (<name of the smartclient service instance>)". If you change the only the portion in the parentheses and save the packaging project you will have to make the same change every time you re-package.
This structure "APM Client (<name of the smartclient service instance>)" is reserved for use for defaulting the shortcut name.
To specify a unique name that will persist, the whole name must be changed to a different format. For example
Remove parentheses: 'APM Client - instance name'
Change it completely: 'APMClient'