Hi Jillian (& Erin!),
We cannot offer support for third party apps but I am familiar with the app as I've used it in my own shop. From what I understand, Etsy On Sale, auto updates your shop prices for the duration of a sale. If your listings are unified, your linesheet prices will also be affected. When your sale is over, your prices will automatically return to their pre-sale pricing. Since your listings are unified, your linesheet pricing should update to the pre-sale pricing as well. If you find this is not happening, let me know so I can dig around.
Unfortunately, there is no way to delete an entire linesheet of unified listings. Deleting items from a linesheet will involve you manually updating the sales channel to each of your listings.
Hope this helps!