Did you manage to manually compile and install the new libxml version? Did you try to restart services after that by running the command below?
sudo /opt/bitnami/ctlscript.sh restart
We have a Support Tool that will gather relevant information for us to analyze your configuration and logs. Could you please download and execute it on the machine where the stack is running by following the steps described in the guide below?
How to Run the Bitnami Support Tool
Please note that you need to paste the code outputted by the tool in your reply.