Please refer to the following KBA: Segger J-Link Known Issues with FX3/CX3/FX3S - KBA229847
Please follow the steps mentioned and see if you are able to successfully navigate through the firmware using breakpoints.
I read through the page you linked, and I don't think those are related. I'm not getting any error codes, and I'm not using J-Link (although I plan to once the prototype board is ready). I'm actually using the CYUSB3KIT-003 demo board right now, which has a Cypress chip that does Jtag to USB, if I've read the documentation correctly.
While I was trying those though, I noticed that if I tried to add a breakpoint while the program was stopped at the temporary breakpoint at the start of main, a message appeared on the console saying "No source file named <path to the file in which I tried to add a breakpoint>." The path was missing slashes between the directories though. It seems like it could be relevant, although I don't know where I could have messed it up.
I also went back to the old workspace to double check, and it still works fine there.
Among other things, today I tried creating a new project in the new workspace to see if I could use breakpoints there, but that didn't work either. It was the same as with the project I imported.
I tried creating a new workspace higher up towards the root of the repository, and copied the project into there. Now I can set breakpoints, so it seems like a path length problem, or something similar.
I know it's not a Windows problem because I've enabled long paths. Whether it's a gdb problem, and eclipse problem, or an openocd problem, I don't know.
Please refer to the following thread with a similar query: Strange behaviour when setting breakpoints (slashes pruning from pathnames)
The interaction marked as the answer and the following interaction can help with your query.
Ah. Yes, that works too, and it allows me to keep my workspace where I want it. Thank you!