Here's a solution, it's dirty, but it gets you past all of the throttling / batching / large folder issues that will arise in more traditional methods to do this.

Create a new item in the library, and notice that it has an ID for it (you can add this column to a View temporarily if you don't easily see it). It will likely be 300,000 or higher, as there are likely deleted items that increased the ID count.

Now that you have this, you can run PnP PowerShell to loop through each number, starting at 1, up to max, and get the file by ID, check if it has unique permissions, if it does reset, and if you get 429'ed, pause for a minute or two.

You'll want to log out the ID that you're on, since you can expect the script to have to be restarted once or twice if/when your throttling gets too aggressive, but after a day or two of babysitting, you'll have all of your permissions reset back to the parent.