Saw a thread on this in AD, but the person said it was solved, all on it's own (no actual fix).
However, in APub 2.0.4, a few days ago I had added a couple vector images from Pixelbay. My prefs for the document were to have Linked resources. After adding the images, never bothered to look at Resource Manager, just kept working on the doc. Over the last several days, have done several Sleeps with this MBP. This morning I was going to export a pdf but preflight said I had missing resources. Sure enough, as reported in that other thread, the vector images from Pixelbay were shown in Resource Manager as "Linked" but missing. Never seen this happen in all v1 versions of APub, so something new! IIRC, any images brought in through the Stock panel were always brought in as embedded no matter what the doc prefs were.
I ended up having to relocate the images in Stock/Pixelbay, drag them in, then go into Resource Manager and change them from linked to embedded.
Gotta be a bug.