As I see it's possible to write some script which will update path to certificate, there is a special event in cPanel which is called when certificate is updated and path to new certificates are passed as params, see documentation here:

https://documentation.cpanel.net/display/DD/Guide+to+Standardized+Hooks+-+Whostmgr+Functions#GuidetoStandardizedHooks-WhostmgrFunctions-AutoSSL::installssl