It should work ok, provided that you don't have any settings persisting in your local directories that are specific to the 32-bit build. If you have copied entire *.conf files in there and only updated a couple of settings, the rest of the default values may have some impact on the new 64-bit version.
In general, using the install packages such as .rpm, .pkg, .msi etc. should all be able to handle this upgrade, as long as you ensure that they are installing to the right location.
To be completely sure, you could move $SPLUNK_DB aside, wipe the current instance entirely, install the new version and move $SPLUNK_DB back, but that doesn't take into account any custom configurations you have made. To do that you would need to presever any local directories too, but again, see paragraph 1 above.
