Just faced this problem, had this happening several times before that target lists imported manually into a project are lost. Only 1 project running at the time this screenshot was taken, seems SER just 'forgets' about a couple of k target lists. Would be great if Sven could look into this. Same happens when a project is set from active to inactive and it's at 8000/12000, the remaning 4000 target URLs are just lost sometimes.
Before it makes this huge jump in the target URLs tracker, it had slowed down to 3-5 threads for a couple of minutes. After another 3-4 minutes, it loaded the remaining target URLs (there's been about 15k more) and continued, but isn't there something wrong according to the screenshot?