nCE pin in PS configuration mode

As I understand, the nce pin disables configuration. But what will happen if it will be toggled during configuration in Passive Configuration mode? Will it temporary stop accepting stream, or will it stop a configuration process at all?

In my application, I want to use the same SPI interface of CPU for reading data from serial flash, and to configure FPGA (Cyclone III). Memory has a CS, so no problem. But what about FPGA - will the nCE pin act as a Chip Select and temporary disable configuration while nCE=1?

Thanks in advance for comments.