If I play Lysandre's Trump Card and I have a Lysandre's Trump Card from a previous turn in the Discard pile does that card get shuffled back into my deck?
No, the wording on Lysandre's Trump Card that says "except for Lysandre's Trump Card" is referring to all Lysandre's Trump Cards in the Discard pile.
Source: Phantom Forces FAQ (2014-11-13), TPCi Rules Team (2014-11-13)

Relevant cards

Note: All applicable cards may not be listed below.
XY4_118
XY4_99