I know this is an older post, but I think I have the solution. I, too, was experiencing the "corrupt file" message when attempting to load a .cyc file, and I didn't want to rely on saving the Cyclone instruments that I created within a track template. That idea could work if starting from scratch and I knew which instrument I wanted to use, but it wouldn't work if either I wanted to try different instruments with a track already made or if I wanted to use multiple instances of Cyclone.
Basically, I loaded in the .WAVs, set everything up as I wanted it, and instead of using Cyclone's "Save" feature, I saved it as a preset from the top of the window (which all VSTi's have). In order to load, instead of using the Open button on Cyclone, I just load the preset from the drop-down at the top of the window. It works perfectly!
I have to admit, even after doing that, it was a little quirky. The first time I saved the preset, the key mappings jumped up an octave. Another time, a WAV moved itself down to a few positions, pushing all the others up one. But I banged on it until it saved the way I wanted it, and it works!
I have to admit, Cyclone seems a bit fiddly in general. It was difficult to align a WAV with a specific note, and trying to get the WAV to respond to anything between velocity 0-127 was also a bit frustrating, but perseverance pays off! I wanted a sampler where I could simply trigger clips from, and Cyclone hits about 90% of what I want.
One note - None of the WAVs I was working in were acidized. I doubt that would cause the "corrupt file" condition, but I thought I would mention it.