You can add a exclusive split in your microflow which splits based on a boolean (PopUpShown). By default you can follow the false path, which shows a pop-up page. On this page you click the Yes or No button and execute the same microflow from there again, only switching the PopUpShown to true so you can progress to the rest of the flow. From here you can execute different logic based on the selection the user made in the pop-up.
It's not the most elegant solution, but what if you split it into three separate microflows? The first one would end with with the 'show page' action. Pass the 'Pakket' object to the page, then on the page, have a 'Yes' and a 'No' button. One of them will delete the old item and one will keep it.
Submit this as an Idea on the Idea forum, you have my vote! :)
I'll do it differently. Instead of having a pop up with a yes/no options, I'll just have a delete all button that checked the Delete boolean for that entity. Having the microflow wait on userinput is not possible either apparently so calling a popup during the original microflow won't make it wait.
Additionally, I can't set a global boolean to call throughout the application which would have made short work of this situation.