That doesn't make any sense. I do similar transformations all the time, and
their running time is always roughly O(n).
H2 basically builds a new table with new data, and then drops the old table and
replaces it with the new.
I suspect you have some other code getting in the way somehow (e.g. triggers,
custom table engines, views, etc)
Try using some performance profiler to see where the time is going (e.g. the very basic one built into H2 should be fine
for this job).
If that doesn't point you in the right direction, please construct a minimal
test case, and log a bug.
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