When creating a SKU in your Amazon Seller Central, you choose an inventory source for that SKU; FBA or FBM.
FBA = Fulfilled by Amazon
FBM = Fulfilled by Merchant
Listing Mirror sees the inventory source that is assigned to your Amazon SKU and will maintain that assigned inventory source. Amazon is the only marketplace that cares about FBA SKUs versus FBM SKUs. Amazon will not accept MF QTY for an FBA SKU and vice versa.
Changing the inventory source in your Amazon Seller Central is NOT the correct workflow for this.
Proper Workflow for Adding a New Inventory Source to an ASIN.
1. In your Amazon Seller Central, create a new SKU that points to the same ASIN. It can even be a similar SKU, but perhaps you had a '-FBA' or -'FBM' to the SKU, so at a glance, you know which inventory source it uses.
2. Assign the new inventory source for that listing. If you are creating a new FBM SKU, make sure to set the quantity to what you currently have in your warehouse.
3. This listing will then be imported into Listing Mirror.
4. Listing Mirror will see that it has the same ASIN as the other SKU, and they will be linked as Duplicate Listings.