They may end up being another deluge of new features. 
The Edit/Find/Project Replace… command is more appropriate to what you are trying to do, but it should be noted that precisely what you are trying to do is not possible to automate since you can only specify one replacement value. While you could use the “RegEx” search option to locate and strip out just the numerals and hyphen, this would not give you a new sequential list of numbers. One thing you could do is replace all of them with <$n>, which is a Scrivener code for a simple numerical counter—keeping in mind you’re going to have to stare at that code in your folder names from this point on.
Or and even better approach, with that counter in mind, you might save yourself a bunch of time by doing just what I described: strip out the numbers and hyphen entirely from all of the titles, leaving only its name. Then go into the Formatting compile option pane, click on the folder icon at the top, then the Section Layout button, and add the counter code there, including the space-hyphen-space after it if you want. Then once you have confirmed that setting, click the “Title” checkbox in the folder’s row (if necessary) to print the remainder of the folder name after each number—style the below preview as you will.
(Alternatively, if you’ve never messed with compile settings before, try a simple preset like “Standard Manuscript Format”) and take a look at its Formatting pane settings. You can examine the codes it uses in the prefix for folders, and change the formatting right in the preview area.
By the way, the search code for stripping out numbers and the hyphen like you have them would be:
^\d+\s-\s
You will want the “Use RegEx” flag enabled, and most likely every other checkbox disabled, save for the “Titles” checkbox. You could pre-select only the folders you want to strip the numbers from, and use the respective checkbox in the middle. (I would also take a moment to use the File/Back Up/Back Up To…) menu command before using Project Replace, especially with regular expressions, as one inadvertent typo could turn everything to mush. 8)
That won’t do anything for the scenes though! Generally speaking Scrivener doesn’t do a whole lot of numbering in the main writing area—for the simple reason that it has a lot of really powerful tools for applying numbers during compile. So that “limitation”, if you will, is something to keep in mind for the future in your naming conventions. Sticking with more descriptive names for scenes instead of binding them to a fixed chapter sequence will keep things more flexible—and you can always add the numbers in when you compile, if you do want them for proofing notes or what have you.
Let me know if any of those options sound reasonable, and if you need any help in finding anything, as I’ve just covered the options here without going into much detail.
