Would you suggest I put them through something like Toast and try to convert it to an .mp4 or .mov file again?
Right idea—wrong application. You still need to be able to acces the a "pro" set of codec components. Basically you can purchase and install FCP X ($299.99), Motion 5 ($49.99), or Compressor 4 ($49.99) to gain access to the ProApps QT Codecs package. Once you install any of these apps, you can run the Software Update utility to download and install the "Pro" codecs package as described in SUPPORT ARTICLE HT4714. Once the codecs are installed as part of your system's QT codec component configuration, they will be available to all media apps that can access your system's codec configuration—e.g., QT 7, QT 7 Pro, QT X, iMovie, GarageBand, MPEG Streamclip, etc. Since you mentioned clients, I assume you are providing a profesional service and might find $50 a fair investment for access to the entire ProApps QT codecs package which also includes other professional editing codec families. In any case, this workflow does provide a low-cost, easy way to leagally install the "pro" codecs on your system(s).
P.S.
You can read DOWNLOAD ARTICLE DL1396 to see which "pro" codec families are included in the ProApps QT codecs package. This may help you better evaluate whether or not you wish to go this route.