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So you're saying, that when I got to Team Plasma and my party fainted, by then being sent to the poke centre, I have glitched the game? I hardly think the developers would have made it impossible to continue the game if you didn't make it through the cave without healing at some stage.
I exited back onto Route 6, before facing N. Problem now is, when Bianca and the Professor catch you (before the Trio find you the second time) they then block the path. This stops you walking out (or in my case walking in)