My mechanic has told me that flushing the tranny fluid on a car that is so close to 100k miles is not good for it. He recommended putting some redline into it, and leaving it alone.

Flushes will help if your tranny is in good shape and you want to keep it that way. After a while, pieces will fall off, it'* moving and griding metal, it'* inevitable. However if you never flush, and after 100k miles of NOTHING done to it ever, there will be crud in there. That stuff will be holding metal pieces together. If you flush that tranny, you're pulling out al the crud holding it together.

Swap out the fluid atleast.

I believe that the tranny has been flushed twice once at 40k, and once at 80k. In that case will another flush hurt it? Also can I still switch to synthetic tranny fluid?

Do NOT use synthetic in your tranny. Especially with those miles on it. If your tranny seems to be in good shape, go ahead with another flush, but I'd suggest changing the filter as well.

If it'* been done, by all means keep doing it, or atleast doing new fluid.

Would a flush be a good idea for a rebuilt tranny with a year of driving on it, about 13K miles?

I've changed my fluid twice since I bought the car. Once when i bought it @ 96K and also @ 104K ( had to replace leaking cooler line ). At 108K it still seems fine so I say go for it.