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Can I use the mysqlhotcopy backup files to different machine which different MySQL version?

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if it's within same minor number of mysql (ie, 5.1.12 and 5.1.24 should be fine, but not 5.2.1) - should work without problems.

if you are going from older to newer version - should work without problems.

for both cases - run repair table on imported tables.

to be on the safe side - preferably set up virtual machine with same version of mysql as source host, restore your backup there. run proper mysqldump and import the date on the destination machine.

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