If your horse belongs to a breed registry you have a much easier job of protecting your investment than those people whose horses are of mixed breed with no registration paperwork. A brand is also a deterrent to horse thieves as long as it is clearly visible of course. The hip or shoulder brand is visible from a distance whereas under the mane is not.
Lip tattoos are about the easiest to alter and they also fade over time.
Microchips are still somewhat new era especially with regards to horses. Any cat or dog being imported into New Zealand MUST have a microchip implant and many people overseas use the microchips in connection with Lost and Found Registries as a means of finding a cat or dog that has wandered off or been stolen. An excellent way of documenting ownership both for registered and unregistered horses is with photographs. Take pictures of your horse from each side and from behind and in front. Take close up photographs of any distinguishing whorls and unique scars.