Safest thing is to replace seals and gaskets while the trans is out, that "filter" is not really a filter in the conventional sense, it is actually a fine mesh screen that self flushes when the engine is shut off. The fluid flowing back out of the valve body washes it out and lets the debris collect in the pan. It doesn't hurt to replace it when the pan is off though.
Standard practice of maintenance service on the trans is a periodic drain of the trans to allow worn fluid and debris out, then refill with fresh fluid. I recommend it at 15k mile intervals. Doing that will keep it healthy. With an install of a used trans, if you don't have a shop go through it, drain as much as you can, install trans, fill with fluid and drive for a few hundred miles. Then take it to a shop and have a flush performed. The 2 bucket method is sketchy at best and can lead to issues. Otherwise, do a drain and fill 2 or 3 times with a couple hundred miles between.
My professional opinion here. I do the drain and fill method with my own even though I have the use of flushing machines at work.