Yes it is a manual replacement
In my first response I tried to indicate that (depending on how much you need to change) it might be easier to simply replace the old words with new un-pointed words. This involves as I said copying and deleting. You should know your own working style and be able to assess if searching and deleting individual vowels is faster than copying and pasting blocks.
For me, I found that copying and pasting the text without vowel points and deleting the previous pointed text was faster than going through and deleting vowels individually. Especially since sometimes deleting a vowel can have strange effects in a word processor.
For portions that require a whole verse or even a significant part of the verse the pop up window is fastest. Just delete the portion of a verse that is not needed.
For one or more words that do not form a significant portion of a verse copying and pasting from the browse window is probably best. The real power and flexibility of BibleWorks ability to copy and paste in one or more versions is harnessed from the BW Options Window.