Twitter has several policies and usage limitations for all across the Twitter network. They don't allow anyone or any program to delete more than (most recent) 3,200 Twitter likes. Their architecture doesn't allow a user (including API) to scroll beyond the most recent 3,200 likes. If you already deleted them by using Circleboom or any other tool, you can't delete your liked tweets anymore, unless you liked them after the deletion. So, you can still delete your new Twitter likes!
The number of likes shown by Twitter after deleting the most recent 3,200 likes includes the very old "likes" count. Even though Twitter shows a number on the "Likes" count section, it doesn't display old likes on your timeline and does not allow anyone to delete those old likes/tweets. This is a Twitter design decision and we can't do anything about it. If it so happens that Twitter changes this rule in the future, we'll definitely implement it.