I am using the 'serial in' (node-red-node-serialport) node and would like to change the serial port settings based on information recieved over mqtt.
However, I do not know a way to change the properties of a node while the application is running. Is this possible to do? If so, how is it done?

It is not possible at this time.
The best you can so for now is...
- have multiple serial nodes setup with a selection of settings & route messages to the desired serial node based on the value set in the MQTT message
OR
- save the MQTT value to ENV VARS & use ENV VARs for the serial port settings (NOTE: env vars are only read on start up so this solution would require you to restart node-red after a change)
How many variations do you expect?