Flooring + backerboard screws + asbestos
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I think you need professional advice. Asbestos is difficult for homeowners to handle on their own. Call you local flooring experts.
Not only removing the screws would disturb the asbestos layer but doing anything to the woody layer would also disturb the asbestos. I am going to assume that the original flooring being asbestos and the wood look layer was installed to encapsulate the asbestos layer rather than spend the money for removal then tiled over that. If the condition of old asbestos flooring is in good condition it legally can be covered with new flooring, underlayment, etc. This is acceptable by the EPA. I would not do anything to the wood layer and install flooring over it. If you mess with it and expose any of the asbestos layer you will be obligated to have it professional removed.
I agree about professional advice. If asbestos is undisturbed and encapsulated I think the term is, then it is safe. The second fibers enter the air, you have a problem. Asbestos also affects home sales and you will have to disclose it if you sell. A floor makes me nervous, because it gets changed more frequently and gets much wear. If you don't want to deal with removal, I would make sure it was sealed and covered maybe with one of the new membranes they have. Proceed with caution.
Use a putty knife and gently rub over the wood layer and sink any screws that are high. You can use lauan plywood over the wood layer. Glue and screw it on. Gives a much smoother subfloor. If your going with ceramic tile use cement board. Strandboard really isn't smooth. If it gets wet it does break down and swell.
Screw the screws down. That probably was part of encapsulating process of the asbestos layer. As long as the floor is level and your going with laminate you wouldn't really need to install any underlayment since you will be using the underlayment recommended by the flooring manufacturer.
If there is enough screw to grip you can use a crow bar or vice grips to remove them. You can also hit them with a hammer sideways to break them and pound the stub down. If they aren't sticking up too much you could just pound them down.