I've used the 'Compact and Repair' function a number of times to 'clean up' a client application before deployment to my users, and it appears that this action only affects the client app itself. There are no 'locally stored' tables in this file, only forms, queries and VB... but I wasn't sure if it would have some sort of knock-on reaction to the linked Sharepoint Lists.
The compact and repair function will only operate on the local database file, even if you had linked access tables, those databases would not be impacted; hence there will be no changes to your linked sharepoint lists.