I”m wondering if it’s because it’s a partition where the images reside. I wouldn’t think that would be the case, but it is possible.
In my workflow, we don’t have the issue of a different job using the same art work from another (except for logos or something). Or if they do share the same art, we copy it to that job.
We have separate folders (including art folders) for each individual job. And that folder also includes the fonts.
So far as external drives, I have a couple I use at home, but that’s mainly for clones of my system, which I do weekly.
But I’m not going to tell you to change your workflow, as apparently it’s worked in the past and that’s what you are used to doing. And if the images are large and take up a lot of space, I could see that packaging them could be a royal pain, and time-consuming.
Something tells me it’s the partition and InDesign is getting lost. Was your previous external drive also partitioned?
Would you be able to put in a second internal hard drive into your computer and store the art on that (instead of an external drive)?
Are you on a Mac or PC?