There are a number of different ways to accomplish this. Simplest way is to put it on a new/edit Page (using a reference selector), and then when the page is saved, your reference will be updated. Using this method, your Employee would see a list of Customers in a Datagrid. Using an edit button pointing to the page I mentioned previously, the Employee could change the reference, save the customer and you are done.
To accomplish this via a microflow is do-able, just not as quickly and easily. Is there a reason you would like to use a microflow? You would build your microflow to accept a Customer object as a parameter and then change the Status association. You could either change the status to a certain status (which you would retrieve in a microflow action with an XPath constraint to get the correct status object), or, if your statuses have a sequence attribute, you could get the next status in sequence using a retrieve action. In either case, the way you change a reference in a microflow is via a Change Object action. In that action, you would select the reference you want to change and specify the object to change it to.
Hope that helps,