Need to migrate from the soon-to-b-obsolete EP1C3T100C6N (Cyclone ) device to a newer one - please suggest how do I do it.

Hi,

Yes, Cyclone II is soon to be obsolete due to declining demand.

https://media.digikey.com/pdf/PCNs/Altera/PDN1810.pdf

Are you looking to replace with 'pick & place holder' or 'similar/better features device'?

Yes, Quartus II 13.0 is the last version which supports for Cyclone II devices.

You can check through the 'Intel Download Center' link below.

http://fpgasoftware.intel.com/13.0/?edition=web&platform=windows&download_manager=dlm3

Thank you.