Can I program an XC3S50J ES part with ISE 6.1i? Are the bitstreams compatible between the XC3S50J and the XC3S50?
No, you cannot program an XC3S50J ES part with ISE 6.1i. The bitstreams are not compatible between these two parts.
The XC3S50 production part has enhanced architectural features and the bitstream is larger. To program the ES XC3S50J, you must use ISE 5.2.03i. For the XC3S50, you must use ISE 6.1i or later.
Programming either part with the incorrect software version will cause a configuration error, but it will not damage the FPGA.