Hi,
i know the conversation is old but I think I found the answer.
In my case, I wanted to use "Update the file properties" action to populate a word document containing fields.

When you use the library properties, it creates new columns in the Sharepoint library => Those columns will appear in the "Update the file properties" from then on

You need to go to the Sharepoint library and delete the column.
I did that and now, this particular properties has disappeared from the "Update the file properties" action
Hope it helps !