If you clear the cache from within Adobe Captivate with all projects closed, there will be little or no risk to any of your project files. Once you open one of your project files in Adobe Captivate the cache files for that particular project will be recreated.
If you wish to select a new location for the cache files to reside, make sure that the location will always be accessible. For example, select a location that is located on your computer’s hard drive. External hard drives may not be a good choice and I would never select a networked location such as a corporate server located elsewhere.
The only time you risk damaging your project is if you delete the cache folders, or your connection to that location is severed while the project file is open in Adobe Captivate. As long as you don’t migrate or delete the contents of the cache while the project is open, your projects will be generally safe.