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I have a flow where i collect JSON-files from an external system, which i use with a JSON pickup to attach to a PDF file as metadata.
The problem is that i often get new JSON-files with updated info and I only want to keep the latest version of that JSON-file.
Because of the unique prefix i can't just overwrite the previous file.
Is there a way to check if a file already exists in a folder within a flow and delete/overwrite the old one?

I think you need to elaborate a little on how the flow works. If you are just collecting the JSON files in a folder and then later picking them up using the PDF you could just leave the JSON files in a folder with no outgoing connection (and overwrite) and then use Inject Wildcard to let the PDF pick up the JSON file. Afterwards use JSON pickup to attach the metadata to the PDF.

Your solution with a folder without outgoing connections and an Inject job worked.
Thanks