How are you attempting to relink the 5D? Are you decomposing and trying to relink to the master clips? That won’t work. The way I do it is, is I’ll separate all my 5D from tape based material and move it all onto one track. I’ll sub sequence that track out so that I now have one timeline with only 5D based material.
Move that sub sequence into it’s own bin, and use the “Set Bin View” option to show all reference clips, and open the bin column for “Source File”. Granted, the 5D file structure tends to make all clips MVI_001 and such, but this will give you a list of source files you need.
Take the drive with your low res media offline.
Then, AMA the source files. In the bin with all the AMA clips, highlight them all. In the bin with the subsequence, highlight it. Right click the sequence and select “Relink” In the top half of the relink box, select the second option which is “Selected itms in ALL open bins”. Just below that, make sure the enable the box that says, “Allow relinking of imported/AMA clips by Source File name”. I generally uncheck “Match case when comparing tape and source file names” and I also uncheck “create new sequence”. Your 5D clips should be relinked.
Here’s were it gets tricky, if your files aren’t uniquely named, it might cause problems. If you have multiple 5D cameras, and therefore potentially have various files called MVI_001, that will confuse the Avid. I have two suggestions to take care of that, but they have to be done before you originally AMA your clips and transcode for offline. I use QTChange (which is available at videotoolshed.com) to add the timecode data from the THM file. This will embed the timecode into the quicktime. If your data wrangler didn’t include the THM, you’re out of luck here, however, my suggestion might still help. Once I’ve added the timecode data to the quicktime files, I rename them to something unique. For example, if I’ve designated the 5D as C cam I might rename the file MVI_001_C01_051712. You can use the free mac application “NameChanger” to quickly change names.
This will get your AMA clips relinked to the sequence. Right click the sequence and select “Consolidate/Transcode” and transcode to your finishing resolution.
Whenever possible however, I try to lay my 5D back to tape. On my current show, I take all 5D footage and lay it back to XDCAM discs and then create my offline media from those XDCAM disks. It made our workflow very smooth. Here is a link to my XDCAM workflow that might be helpful for you.
https://f1.creativecow.net/3954/xdcam-ama-workflow-guide