How to "merge" syncs?
At least for contacts it's easy: the contacts app offers "export to SD card" (resulting in a .vcf file) and "import from SD card" as well. I'd do that first anyhow, so if something goes wrong you still have that.

The calendar app unfortunately doesn't offer a corresponding option – but there are some calendar backup apps which should be helpful (check that page for other backup apps as well to cover things you might have forgotten to mention).

WhatsApp will be trouble here I'm afraid.

Apart from the above, calendar and contacts should merge fine if you use either Google sync or your own DAV resource. Still, it cannot hurt to have a separate backup :)