Not sure why putting new paste on would do that but it does mean you disturbed the cooler as well disconnecting it.
Would you say if you feel both pipes you have one hot pipe and one cold pipe. This would indicate fluid is not moving as normally temperature evens out as fluid mixes so quickly round the system
On the pipe that is hot is it same temperature all the way along from the CPU right up to the radiator or does it get cold all of a sudden.
With system running if you place hand on pump can you feel the vibration of the impeller. You might need to increase pump speed if you are controlling it to a higher rpm to see if you can feel it. If you cannot feel it then suggest pump not functioning.
I assume at some point everything was working or has been, what was done just prior to the start of the issue appearing, maybe that might shed some light.