After having a discussion with David from Redgate, we have come up with a workaround to do exactly this, until a new feature is added to Sql Refactor.
If you go into the 'object explorer details' pane, highlight multiple stored procedures, right click and choose to script a "create to" window. Then do a find and replace on the whole script changing "CREATE PROC" to "ALTER PROC", you can then choose to reformat this one script, and run it.
The only problem with this in my case is that I have several thousand SP's, so it can take some time to actually create the long script. Something like 10 - 15 mins!
But it works.