It is "possible" that Lightroom 6 did not upgrade your old catalog like it should have. I suggest that you try File->Open Recent and see if another catalog is listed. If it is, click on the other catalog and if LR 6 offers to upgrade the catalog allow that to happen.
Did the Lr5 catalog get upgraded or was a new one created when you upgraded??
Your Lr5 catalog should be in the Pictures Folder in a Lightroom Folder,,, it ends with .lrcat and if you double click it it will open with Lr6 and a copy will be upgraded for use with Lr6...
Sorry I misled everyone in - I've been dealing with this for too long.
This is happening on a Macbook pro with the latest OS.
Out of 6,800 photos less than 100 appeared after the upgrade, 6,700 were unaccountable in LR6. The Lr5 catalog was updated, only the stand alone photos in the pictures folder appear and all of the photos in the pictures folder subfolders are missing.
In Lr5 I was always able to plug in an external drive and work from it but Lr6 does not see any external drives connected.
LR6 should not need the external drive connected to do the migration. (Generating the previews, yes; migrating the catalog, no.)
That said, try connecting the external drive then migrating the LR5 catalog again by opening it in LR6.