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Already fixed. Use the dev build or wait for the next release.

If you open up the Personal Stats Editor and scroll through the dropdown menu, are there any lines where instead of a name it's just " - xxx" for some number xxx?

PKHeX is open source, you can see its conversion routines. Overriding your settings to No will skip updating things to match the save file. Eggs from other trainers must be traded, so they must be updated to be met as a link trade egg instead of from daycare. Handler states and memories must be adjusted as if a new (or previous) trainer is handling it. When no, it skips doing all that, which lets you inspect the original values. Again, you shouldn't need to override it.