UART stops working after changing core

Clarification: the uart is not the primary problem. The download is either failing at some point, or the downloaded code is no good. When using the \s core, I can't debug or even toggle a pin. I moved my project to Q4.2/NiosII1.1 and I get the exact same results, \e and \f core are fine but not \s. Thinking there must be a problem with the project itself, I compared ptf files.

For both e and f core there are a couple of lines that read:

JTAG_Hub_Instance_Id = "0";

But for the s core this value is "1". This value appears to be assigned during Generation. I thought the difference suspicious, so I

manually changed it to "0" before compilation, but all I got was a project that could not be downloaded, "There are no Nios II CPUs with debug modules available....".

There must be something wrong in one of my project files. Any ideas short of rebuilding the project?