Hmm, good question. I cannot think of a good way to achieve this in the UI but it would be relatively easy to do this directly in your project database (Tropy's project files are SQLite database files). The only tricky part, really, would be getting the ids of all the photos you want to delete, but if, as you say, you know that you want to remove every PNG it would be very easy.
SQLite is pre-installed on macOS and is part of every Linux distribution to the best of my knowledge. I have little experience installing SQLite on Windows; I have recommended installing DB Browser for SQLite in the past and this has been well received. Anyway, if you want to try this, please make a backup copy of your .tpy file (just to be safe!), open the file in SQLite, and follow these steps:
> select id, path from photos;
# This should print the id and path of every photo in your project
> select id, path from photos where path like '%.png';
# This should print the id and path of every PNG in your project.
# If this works, we're set to go!
> insert into trash (id) select id from photos where path like '%.png';
# This puts all the PNGs into the trash. This is the only command here
# that actually modifies your project.
# Note that we select only the photo id here, not the path like we did earlier.
> select id from trash;
# This prints all the ids currently in the trash.
# This does not do anything, but you can use it
# to check that the photos are really in the trash.
At this point you can quite SQLite again; right now the photos are still there but Tropy should not show them anymore and the next time Tropy closes this project, it will completely remove those photos and all their metadata. So, basically, all you need to do is open the file in Tropy (be sure to open the file you modified and not the backup copy) and check if the PNGs are gone; if they are, close Tropy to see if there are any errors and you should be all good.
I can also run these commands for you if you want to send me your project file.