I don't think you have correctly stated the model of your camera. Could you please clarify? Here is a link to a list of all the cameras currently supported by Lightroom and Camera Raw, as well as which version of either is required to support your camera:
Yes, I have the most current version of LR (6.8 version). And camera is a Canon mark II 5D, which is on the list of camera supported by Camera Raw. I've been uploading my pics into LR for a few years and never had an issue like this before.
Then check the Destination folder to see if it has the proper read & write permissions.
Ok. How exactly do I do that?
You use the Get Info command.
Select the folder you are reading from or saving to in the Finder. Hold the Control key, click on the folder an choose Get Info from the drop down box. You will see a window like this appear. Look at the setting for Sharing and Permissions, it should say Read&Write for your user account. Change it here if needed.
Tried all this. Still showing only only a few of the photos (out of hundreds) and they appear as CR2 during import, and then I get the same error message after. How is it possible for all those photos to disappear off the card?
Are these images on the camera and are you connecting the camera directly to the computer (If you are use a Card Reader) or on your hard drive, internal or external?
What option are you using in the Import dialog window? Please show a screen shot of that dialog window.
The files are not recognized by the raw format support in Lightroom.
This is not a permissions error. This is not a Destination folder error. This is not an error due to the fact that you have selected the wrong options in the Import dialog.
This is an error due to the fact that you think you have Lightroom 6.8, but you do not. Please confirm (show us a screen capture) that shows the version number under Help->Systems Info.
"I then got a new SD card (in fear the other was corrupt) and updated my Lightroom to LR6.....camera is a Canon mark II 5D,"
There seems to be a huge amount of confusion here and several points on which clarification is needed.
1. The Canon 5D Mark II does not use an SD card. It has a single card slot and that slot is for a CF card. Although there are adapters available for fitting an SD to a CF slot, using one is not recommended because they can cause file corruption.
2. The 5D2 is a relatively old camera, released in Nov. 2008 and first supported by Lightroom 2.2 in Dec. 2008 - more than eight years ago! There is no way that any version of either LR5 or LR6 would not support the CR2s from that camera.
"...they appear as CR2 during import, and then I get the same error message after."
What is that message?
"How is it possible for all those photos to disappear off the card?"
It shouldn't be possible. LR only copies files from a card, without moving or deleting them.
I have a Canon Mark D II and Lightroom 5, and operating on a Mac. It started when I was uploading pics and they came up as CR boxes instead of pictures, and then I started getting the error message "The files are not recognized by the raw format support in Lightroom."... and updated my Lightroom to LR6.
Since you did an LR5 to LR6 upgrade, both versions of the program may still be on your system.
Sometimes the install program does not update your desktop icons correctly. When you run LR, make sure you are getting the version 6 instead of the version 5.