Thank you for that explanation – it explains a lot. And yes, the contents of the clipboard are changed.
I use ClipboardHistory by Agile Route. I tried adding PopClip to its ignored apps list, and restarted CH, but it still happens. No doubt because CH is only looking at the frontmost app for its exclusion list.
I don’t see PopClip putting back the original contents of the clipboard, if that’s what you meant. Experimentally, I quit ClipboardHistory and then applied PopClip to some selected text. It still copied it to the clipboard, without doing an explicit Copy command. So it doesn’t appear to be Clipboard-History-specific. I experimented in Mail, TextEdit, and Safari (under Catalina).
Did I misunderstand what you meant about PopClip restoring the contents of the clipboard?