I found a hacky solution.
I'm assuming you already have an iOS app released and would like to get rid of a macOS or tvOS version with the infamous Prepare for Submission status.
Step 1 - Head over to App Store Connect > select your app.
Step 2 - You'll need 3 versions for this to work - an iOS version, a macOS version and a tvOS version. If you're missing the macOS version, tap on Add macOS App (on the left side) to add one. If you're missing the tvOS version, tap on Add tvOS App to add it also. You don't have to add any actual builds to each. You should have all three versions like below:
Step 3 - To delete a version, make sure that it's not selected. For example, I want to delete the macOS and tvOS versions so I selected the iOS version instead (screenshot above). Click on the iOS version to select it and refresh the page.
Step 4 - If you hover above the macOS or tvOS versions, you'll see a small ⛔️ (remove) icon on the right side:
Step 5 - Clicking on the icon shows you the popup to Delete the specific release (macOS or tvOS). Example (for tvOS version):
Here's the problem:
If you delete either versions (the macOS or tvOS), you won't be able to delete the other one. So if you delete the tvOS version (and remain with iOS and macOS versions), you can't delete the macOS version. It seems like the ⛔️ (remove) icon only shows up if all three versions are available.
The solution:
Step 6 - If you already deleted the macOS or tvOS version, please repeat Step 2 to re-add it again, and also repeat Step 3.
Step 7 - Duplicate the tab.
Step 8 - In the first tab, click on the ⛔️ (remove) icon for the version you want to delete. For example, macOS version.
Step 9 - In the second tab, click on the ⛔️ (remove) icon for the other version want to delete. For example, the tvOS version.
Step 10 - Go back to the first tab and click on Delete to confirm.
Step 11 - Go back to the second and click on Delete to confirm.
Step 12 - After deleting both, you might see a duplicate release (in either or both tabs) for the existing / remaining version (iOS in my case):
Step 13 - Just refresh the page and it should be back to normal:
It's a convoluted solution to fix a problem that Apple should've fixed years ago, but it worked for me.
I hope it helps!