I can’t answer your question because I don’t know the reason of deleting the feeds. I heard about these cases for CyberSEO Lite only and there are no reports for the Pro version. However since I don’t know the reason, I can’t tell anything for sure.
Theoretically any theme or a 3rd-party plugin, which runs at your host may do this. It may use the CyberSEO functions to do just everything… in a same way as CyberSEO may use its functions too. For example, CyberSEO uses functions of the WPML plugin to switch the language.
So if some rogue plugin developer would like to sabotage CyberSEO or any other plugin, he will do it w/o any problem. WordPress does not protect plugins and themes from affecting each other.
Also it may be caused by an unwitting error in a 3rd-party plugin. E.g. if it doesn’t use WordPress API and works with your database directly. CyberSEO changes your database via WordPress API only, but not all other plugins follow this rule.