You shouldn't have to update the AXL that servers use internally. If it's sending 9.0 when all your servers are 12.5.1, that would be a defect, perhaps caused by a incomplete or corrupted upgrade. If you're sure all your servers are 12.5.1, I suggest opening a TAC case.
If you're talking about YOUR use of AXL, then yes, you need to change "http://www.cisco.com/AXL/API/9.0" to ="http://www.cisco.com/AXL/API/12.5". I don't know how you're using it - maybe you need to change your code, or if you're using SoapUI, load up a new project with the 12.5 WSDL.