I may have missed something since this was first posted in 2016 but I have a similar issue with hundreds of Red raw files. As you may know Red spans its clips every 4G so can make multiple clips inside a folder depending on the length of the shot. It also uses a new folder for every shot – every time the camera record was switched off and on then there is a new folder – result: hundreds of confusingly named clips inside hundreds of confusingly named bins (obviously a system designed by a very clever idiot). I can live with that because importing them into premiere pro via the browser it only looks at automatically reconnect clips and treats them as one normal clip.
But now the problem starts with proxies because when you tick ‘put proxies alongside original files’ when you generate the proxies it writes a set of proxies to each individual folder containing those spanned Red clips. So now you have hundreds of proxies each in hundreds of individual folders alongside their clips. These can only be attached one at a time – trying to do so as a batch usually causes the programme to crash and in any case it can’t do it.
However, I went back to the drive and took out all the proxies and put them in one folder – tedious but not as tedious as relinking hundreds of proxies one at a time in PP. Once in one folder PP can find all the proxies as a batch and relinks (AKA ‘Attaches’) them.
Maybe I should have ticked something else when making the proxies if I had known – written them all to one folder for automatic attachment? Maybe that will help you if you are doing proxies for Red and want to attach batches of hundreds.