Debugging active serial programming issue

In AS programming, the FPGA is not shut down, just the FPGA AS-interface tri-stated by driving nCE high.

If you have also a FPGA JTAG interface available, you can try to write the flash through JTAG indirect programming instead.

If you say, AS programming has worked before, what did you exactly change? PC software (e.g. JTAG drivers), board and programming hardware can matter.