Did you import using the 'Move' option?
Which exact version of Lightroom?
So I imported directly from SD card by clicking Import-> using "Copy" option to external hard drive in a newly created folder.
Im using Lightroom CC 2015.6 release
Can you work on them in LR? I mean in the develop module, not in the library.
Do you get any message that the file is missing when you switch to the develop module?
If not, the file is there. In the library, select an image and right-click (on PC .. equiv on Mac), select to open the location in finder.
Do a test import and take notice of the exact path to the folder you are creating in the Destination area. I suspect the Destination area is pointing to some other folder than you think it is.
Do the images show up in the LR catalog?
Do they or don't they have a Question mark next to them?
If you right click on one of them and select Show in "Finder"/"Explorer" (Mac or Windows) is the actual PATH to it the same as you thought?
So my problem is that the folders that the images should be in are not on the hard drive anymore, they just vanished. Two somehow reappeared again, but they keep disconnecting in lightroom. So all of the folders are with question mark, when I try to link them to the few folders that didn't disappear, it starts telling me, that the corresponding photo is already linked to its file.
at some point one folder finally connected and lit up white, but it comes and goes.
So when i right click the images to see their location, it cant show it to me, because the folder on the drive is not appearing. when I manually open the drive in finder, a lot of folders are missing. And I know for sure, that I did not delete them.
I also just did Test import, and same thing happened! this time i created a folder in finder with a test image, then dragged it to light room, it imported, but instantly the folder in the lightroom library showed up with a question mark and when i tried to located manually the folder, it was not showing up
Since I'm not a Mac-user I feel I can not help you. The drive seems to somehow disconnect. You are not able to work on the images also since they have an exclamation mark.
I don't think that this is a Lightroom issue. IMHO, it's OS and/or drive related.