I don't know what the root cause of your problems may be, but I just encountered the same error message several times ("Failed to resume target process, Downloading ELF file"). It persisted through a project clean/rebuild, power-cycle of target, and power-cycle of workstation. I was trying to debug a program that I had been successfully downloading and debugging two hours earlier today.
It appears that my solution was to create a brand-spanking new project, and flash it to the target. I got the ominous "secure flash bit" warning or whatever it is, hadn't seen it in a while, but I clicked through and debugged the new app. I then closed it, re-opened my earlier project, debugged it, and it actually decided to cooperate and download to the target this time.
I had earlier tried debugging a bootloader-style application directly, which is probably not allowed. But that attempt apparently left the target in such a state, that the tools had no idea how to deal with this condition, and just threw up a useless error message. I'm really getting tired of dealing with beta-quality tools.
