Joe, you are correct in that if you flip them then the toungue will not align with the groove. The other thing is nails in 1 board and you will destroy a set of planer blades. I don't think any mill would be willing to run them for you either. They can be thickness sanded also, but might have the same issue with nails.nails.
The best bet would be to drum sand them after reinstalling them, then the walking surface will be nice and even.. Also you are not going to have the same amount to put down as you remove due to breakage. If you plan on milling them yourself it will be a long time before you get to ride another bike.
When you pull them up they are probably blind nailed at the tongue, good way to do it/hard way to remove. This may cause a lot of the boards to have the tongue broken off. Go slow and easy when you demo.
Good luck!