Why does "Signal Probe Pins" take 3 times as long as normal project compilation?

If you are trying to probe deep signals in a design that uses a lot of routing, it may take longer to find a way of routing the signals out, but 1 hour is pretty excessive. How many signals are you trying to bring out and how big is the design? Is the Signal Probe compilation successful after that hour?

Signal Probe pins are lost after a recompilation of the project because, as you mention, this is an ECO change based on the final compiled netlist, which changes after you recompile. You can run the signalprobe_qsf.tcl script generated by the tool to restore them. If you are using the Standard edition of Quartus and if you use the incremental compilation feature, you can also maintain Signal Probe pins if you put the Signal Probe nodes in a design partition and choose to reuse the post-fit netlist.

#iwork4intel