It should be acid washed to stop any current corrosion. A sealant should be applied around the edges during installation, to prevent any moisture from penetrating between the two sheets' surfaces. It may be overkill, but the application of a primer to both interior facing surfaces, would ensure a long lived repair.

Gard

If there is an open air space between the sheets, that might work. However when two sheets are stored or assembled face to face, moisture will wick between them and because there is little O2, the metal can't oxidize and it quickly corrodes.

The airline I worked for took delivery of some 6 and 7 thousand series aluminum T6  4' x12' sheets, .060" thick. The guy driving the fork lift on the receiving dock was busy else where, and the sheets were stacked on the side of the concrete platform out of the way. This was outside, but under cover.

Somehow they sat there for a couple of weeks before they were brought into receiving inspection. When the inspector lifted each sheet, there was an accumulation of white corrosion on the surfaces of each one. The whole lot had to be destroyed so it could never be used on an aircraft.

In Nam, the mechanics had a particularly hard time keeping the aluminum available for repairs. If any metal were stored face to face (stacked), because of the high humidity and lack of air, the metal would start to deteriorate in a matter of weeks. Each piece had to be stored with spacers between them, like air drying rough cut wood.

So, if the space is open, the holes would allow a circulation of air which would enable the aluminum to oxidize. If the metal is touching face to face, a hole in one would allow moisture to penetrate. Without an air circulation, this would cause it to deteriorate.

In the commercial aircraft industry, any aluminum assembled to another, is surface primed first. Zinc Chromate primer is the most commonly used product. It is tough of the body, and a good respirator is necessary whenever it is sprayed. Brushing it on isn't as bad. There are many self etching, epoxy, automotive primer brands that work well on aluminum. This is what I would be using on any bare aluminum contact.

 Just my $.02    Gard

I don't know how bad or what your floor looks like, but I believe I would patch the holes (either weld them closed or patch over with small pieces of aluminum, etc.) Then take the trailer to R.T. Smith and have a W.E.R.M. floor installed...  http://www.selecttrailer.com/WERM.html  That deal of putting aluminum over aluminum ain't going to work too good, Weight of the horses on it is going to make the edges turn up.... They ride on it long enough the aluminum will stretch, corners turn up, looking like a giant WOK...!!

Some pictures of that bad floor would be nice....

3M makes a marine polyurethane adhesive/sealant 3M5200. It has one of the strongest cured shear strengths of most similar products. In marine construction, many structural elements can be affixed using this product and no mechanical fasteners. It has a wide range of elongation without tearing or bond failure. The only downside is a lengthy cure period.

If this product were continuously placed around the perimeter of the two pieces of metals, and between them in at least a 1" line, it would almost certainly hermetically seal the metals sandwiched together. I assume that hardware will also be used to affix the new panel(s). This and a precoated primer should make a life time repair. 

The new panels would crush to match the supporting old, and you should have a strong piece of flooring. If an additional step of applying additional 5200 were made, in a one foot grid pattern over the surface of the repair, when cured, the two metals would be permanently bonded together in multiple spots. This would eliminate any future separate oil caning or movement of the individual metals.

However if the newest piece of aluminum were to be removed, it would be impossible to do so while remaining intact.

Gard

If you check the specs, you might find they instruct that 3M5200 is moisture cured. If you live in a particularly arid area, it might slow the curing process. I live in an area that has a variable rate of humidity from 50% -100%. I've used gallons of the stuff and only had one bonding problem. That was a mechanical failure, caused by a worker who installed the sealant over a gell coating, that was not cleaned of mould release wax, after the boat hull was pulled from the mould. 

Regardless, using the best product you can purchase, will provide a better and longer lasting repair. An epoxy product should give you an excellent bond.

I would include the use of stainless screws on the perimeter, to hold the panels together in alignment while the adhesive cures. I would also incorporate many sand bags or other heavy objects located at every available surface space, to press the new panel onto the old, to ensure a proper contact and bonding.

BOL  Gard