quartus_map fails with "17942 No Open project exsists" after adding probes

Instead of copying the project over to a new directory, have you tried simply disabling, at least temporarily, Signal Tap from the project Settings? If you can synthesize the design without Signal Tap, then something is messed up in your .stp file. Are you trying to tap pre-synthesis or post-fit nodes? In most cases that I've found, pre-synthesis is the way to go.