@chaithuj first: make sure to always have a backup of your work on another machine especially if it is unstable.
Then you want to check the resources of your system. Larger workflows will need more (especially) RAM. How many GB do you have assigned to knime? What is your operating system and processor? Make sure knime has enough and no other program is running at the same time.
You could try and activate columnar storage in a copy of your WF and test that (you remember to backup?).
Then: you might have to think about restructuring your WF and maybe call several parts from one central one.