Using Flow to get or check for files in a large SharePoint library can be a little tricky. If you are sure your library will always stay under 5,000 items the Get Files (properties only) Flow action is a quick n’ simple approach to use. When your library crosses over the mythical 5k mark or somewhere in that neighborhood, the Get Files action will fail to return results without warning. What I’m outlining below are other options when working with large libraries.
Setup:
Option 1: Get Files using an Odata filter query
downside: only use this in small libraries
Result:
Option 2: use the SharePoint API
downside: the lack of transparency from Microsoft related to how often data is crawled. 
Result:
Option 3: use the SharePoint API along with a filter action on the library. This option does require that you have metadata set up on the library to filter on.
downside: you will need to set up your metadata ahead of time or create it after the fact then backfill.
Result:
The more I learn about Flow and SharePoint Online, the more I’m starting to like Option 3. SharePoint Search is an extremely powerful tool if the search index is fresh.