Omnivore - workflow for using content?

I’m using Omnivore to get content into my vault. It works well. However, once in the vault I like to work with the content - highlighting, tagging, linking beyond what is possible with Omnivore alone. The problem is the Omnivore plugin might overwrite my work if I use the imported file for this purpose so I would lose all the additional changes.

Does anyone have a workflow for using Omnivore (or similar) imported content further?

I could just make a copy of the imported file, although that would create a duplicate in the vault. I considered using the Note Refactor plugin to extract content elsewhere, but because the Omnivore file might be overwritten the link with the original source would be broken.

In my current workflow, I do all my highlighting in Omnivore and the pull only the highlights into Obsidian. With the most recent version of the Omnivore plugin, you can also sync the full article/text and Obsidian will show the highlights you made inline.

Once I have this in my vault, I can link to it from my personal notes as I’m putting things in my own words into my PKM system. So far this is working well.