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The safest way to do this is probably to obtain a dump of the entire database and manually move it to the other server. I have found that doing it yourself ensures that it gets done properly, and that no data is subject to possible loss.
In theory, WHM transfer does it perfectly - but I personally do not want to leave data to chance erasure or loss. And always back it up in at least 2 different locations (or if the database is too large to do that with, backup only 1 copy of it somewhere - or do whatever you want).
I have never used WHM to do db transfer, might try it next time I need to do that.
Cheers
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Chris Jordan
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