Hi @toshach!
I don’t think you are using KNIME in a incorrect manner and even better news is there is no need to reset all child workflows each time as they shouldn’t be saved after execution. What seems is happening is when re-running the parent workflow without closing it first. As @mlauber71 picture shows then there is green dot left on all of your child workflows(after first execution). In this case child workflow is in state executed and re-running parent workflow won’t have effect of course. Resetting parent workflow doesn’t help here as connection between workflows is left (green dot is still there). Solution would be to close parent workflow and re-run it then. Your table should be updated 
Regarding calling KNIME in a batch mode using nodes calling other workflows check this topic:
Br,
Ivan