Loads of people are having problems with LR6 upgrades. So did I two weeks ago, when I first upgraded my LR5 catalog, letting LR6 do its own thing.
But now I have LR6 working reasonable well. How did I do that?
From bitter experience having upgraded LR many times from LR1 onwards, I have found that several things contribute to a good upgrade.
1 The first thing to do is to disable your LR5 Preferences file. Just rename the last part of it to anything except the normal .agprefs. If you don't do this, LR6 will simply copy all the stuff in your LR5 prefs file to a new file and label it LR6 prefs. That is NOT a good idea - I don't understand why Adobe still do it. It saves about 5 minutes of your time, resetting your prefs and view options in LR6, but may cause you many hours of despair when LR6 doesn't run properly. It might be OK if the Prefs file just stored your prefs, but it doesn't; it stores all sorts of stuff about your past use of LR5. And LR6 might not like some of that. Simply deleting the LR6 prefs file is not the answer if you have older versions of Prefs files which LR6 will cannibalize.
So disable the old LR5 Prefs file (don't delete it in case you want to go back to LR5).
2. Then install LR6, and tell it to upgrade your LR5 catalog. When it has finished, close LR6. You might then like to move the new upgraded catalog to a new folder labelled LR6, and give it a more sensible name like LR6Catalog, instead of the LR5Catalog-2 that is the default.
3 Now double-click on the newly named LR6 catalog in its new LR6 folder to run it in LR6, and go to Prefs and Catalog settings and set them all up as you want them. At this point I also purge the Acr cache in Prefs, to clear out all the old cached files there (I've been told this is not necessary, but I prefer to play safe.)
4. Now select All Photographs and then go to Library/Previews and tell LR6 to build ALL standard previews. That will take a long while if you have a large catalog (with 95K images mine took a day about 36 hrs. When it has finished (and I prefer to leave the computer alone until it has) you have a nice fresh set of previews and their previews.db and rootpixels.db databases, which avoids more problems if you try to use the old LR5 previews.
Hopefully, you now have a working LR6 system! I have, and even have the GPU working with its latest driver.
There is one other thing I have had to do in the past to get an LR upgrade working smoothly, and that is to export the old catalog to a new one (without previews, images or anything) before upgrading it. The reason for this is to get rid of any rubbish in the old catalog that may interfere with the new version of LR. I know there shouldn't be 'rubbish' in the old catalog, but no program is perfect, and such things do occur. I've compared an old catalog with an exported one (using a catalog browser) and seen the stuff that has been left behind. And it has cured some problems in the past. It may not be necessary every time you upgrade, and I didn't do it this time, but if all else fails, it is worth a try.
I have never done any of these things, and I have not had a problem upgrading catalogs, starting with the upgrade from LR 2 to LR 3.
Aren't you a lucky one!