Are those columns indexed? If so - then most likely the reason for the issue is that SQL Server is performing logical consistency checks on the spatial indexes and that is why they are taking so long.
You could try using NOINDEX to see if that improves the performance of the integrity check. If that does work - then there may be an issue with one or more indexes that SQL Server is trying to reconcile and it is taking a long time. It might be possible to drop and recreate the indexes - but that could take a very long time.
Problems are opportunities brilliantly disguised as insurmountable obstacles.
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