You can specify a different FYV by depreciation area. However, the beginning of the FY and the end of the FY must be the same dates as in the FYV assigned to the company code. The individual periods within the FYV can be defined differently but 1st day and last day of the FYV must be the same
Please search the discussion boards and SAP notes. There is much written about this topic.
Look at SAP note: 844029 as a start. If you are using "new" asset accounting there are differences.
