If you have multiple warehouses in Flexi and need to consolidate them into a single one, the easiest approach is to use transfer documents to move all stock out of the individual warehouses and into the one selected warehouse.
Alternatively, in the Goods module — Warehouse List — by opening a warehouse — on the Administration tab, you can restrict the validity of individual warehouses to a specific date, for example up to the year 2017. Once the following accounting period is initialized, those warehouses will no longer appear in subsequent accounting periods.