Lost root when upgrading from CM11to CM12.1 I recently upgraded my encrypted Nexus5 CM11 to CM12.1 and now i need to reinstall Google Apps.

unfortunately it seems to have lost root access which is needed to to install a zip in recovery mode. i am using TWRP recovery, which does support encrypted storage.

also since i can only get root back via recovery mode, i am now in a deadlock, right?

anything i can do?
Open the development menu in your main settings(to enable it go to About menu and keep pressing the build info until is enabled) and check there that Apps have administrative privileges.