Hello Matt,
Could you please provide a single .CR2 file that doesn't load into PhotoScan 0.9.0, but works with version 0.8.5 so we could check and probably fix the compatibility (please, send the sample file to support@agisoft.ru).
Moving markers from one project to another (based on their projections on photos) could be performed by custom Python script. If you wish (and if the .CR2 files support could not be fixed fast) we could provide you such scripts.