When editing work order parts, you can edit the Is Stock? and Warehouse fields on work order parts even if the work order is locked (such as when using progress invoicing). (All other fields are still disabled and cannot be changed.)
All work order parts coming from a completed proposal will default to Stock? = YES and use the default warehouse set on the Preferences page (Setup > Company > Preferences > Inventory tab > Main Warehouse field).
The Parts Issue screen (from work order parts issue) will only display stocked parts; non-stocked parts are filtered out automatically.