How can/should I harden the trailer to prevent break-ins?

I have hauled trailers that carried thousands of dollars worth of tools. Depending on the trailer there are several ways to harden it against break-ins. one way is to add heavy metal stripps and plates to the inside of the trailer at locking points.

How do I keep the trailer from being stolen in its entirety? Would locks/chains be sufficient?

There are several kinds of locks for the tounge the best ones insert into the area for the ball.

Could I safely carry enough fuel in the trailer (perhaps 100gal) for a long distance bugout?

If your taier has vents cattying fuel in an emergency should be fine, but during normal times check local laws.

How should the trailer be disguised (or can it be disguised) to hide the fact that it contains valuable bugout/survival supplies at a time when the contents would be needed by nearly anyone I encounter? Perhaps load the back of the trailer with frivolous junk so as to obscure the real contents?

disquiseing it is not really an option. Instead of carrying frivolous extras cover important equipment with clothes and lesser important items

What is the possibility that some government official might retain or sieze the contents 'for the greater good'.

Not a real possibility during a local emergency but if it was a large scale emergency the possibility is there.

Am I increasing the likelyhood of breakdowns by carrying the additional weight of the trailer? Should I add to the weight of the trailer by bringing repair equipment (additional spare tires, replacement belts and hoses, etc)?

Some repaire equipment and parts is of course required but don't go over board.
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