That is working as expected. Specifying "\3" like that just says "use the third group in the match". It isn't removing the group from the original. And, you can only update one field at a time. You will need to do it in three steps.
First, set the series name. How you do that will depend on where the series name is. If you are updating books in the same series, you can use the bulk metadata editor to set it. This will also set a series index according to the options you choose at that time. If the series is somewhere in the metadata, you will need to do a search-and-replace to set the series name.
Then, set the series index. Use your search above with the "Destination field" set to "series_index". The "Replace with" will be "\3".
Then remove the series index from the title. Your search above with the "Destination field" set to "title" should work. The replace looks like it should be "\1" or "\4" or something like "\1 - \4". It depends on exactly how the titles are currently structured.
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