If then else is another matter and there are other nodes for that.
With loops there are tow important End nodes.
- one would collect i a KNIME table whatever output is there (you can allow changing structures)
- the variable Loop end would just end whatever is within the loop and just store flow variables with possible informations in them
My impresssion is that you might want to take a step back to the drawing board and make a plan what you want to achieve and familiarize yourself with some KNIME nodes and concepts mentioned in this thread.
Regarding automation / scheduling you have these options
- KNIME server (possibly via AWS)
- Batch mode via CRON or Task Manager
- a wait construction I showed above