If your CPU cannot handle it, it's quite simple - you either need to get a more powerful machine or make your flow process less files at once. Add some delays or something like that. Process the files one by one, instead of all of them at once.
PAD consumes some CPU resources on its own, too. So, it is quite normal for it to require more processing power than it would if you were doing the task manually.
If it crashes completely, you might want to check the Application logs under the Windows Event Viewer to see if there are any errors there at the time of the crash.
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