I have dark/ light areas on stained blotchy birch. I used a prestain cinditioner, how can I fix it or start over?

If you are refinishing it, after stripping off the old stain and poly and varnish and whatever else is on it, use wood bleach per the directions. You can find wood bleach with the other wood finishing products. Then sand smooth and refinish it.

If the stain doesn't lift completely, bleach is again. You can hide a faint discoloration by using a bit of colored stain - it won't be perfect but it will blend it in a bit better.