First of all, without beating a dead horse, you should not remove the transmission and leave the torque converter attached to the engine; the snout of the converter engages the trans pressure pump, and the trans front spline engages into the stator assembly.
In the process of pulling the heavy trans back, it is very easy to bend or damage either of these, making the unit useless. The torque converter should remain on the trans when it is separated from the engine.
That said, if you have all six bolts removed, and the converter is still "attached" to the flex plate after the trans is removed, it is probably just stuck to the flex plate. Notice the two longer bolts in the photo above? If you insert these from the snout side of the converter, you should be able to rock the converter back and forth slightly until it releases. When it does, just remember that it still contains a lot of fluid, so watch how you handle it.
When you put the car back together, you can used those long bolts to get the converter fully engaged with the Tip before mating it to the engine. Once attached to the engine, use a 5/16 rod (see the photo) to hold the converter while you put the converter to flex plate bolts back in thru the starter opening, pulling the rod and rotating the engine (clockwise only) until the next set of bolt holes show up in the starter opening. One very large caution: Be very careful not to drop any of the bolts into the bell housing during this process, otherwise you will have to separate the trans and engine again to recover them.
Good luck............