The latest versions of CellProfiler (5811 and above) have the ability to run multiple pipelines serially. Go to File > Run Multiple Pipelines and it will ask you to provide a directory where the pipelines are located. The function assumes that the pipelines are either located all in a root directory or in subdirectories under the root, so you’ll have to organize your pipelines/folders accordingly. After that it will show a list of all the pipelines it found and give you the choice of running any or all of them.
Hope this helps!