Incorrect. The entire combo gets encored and the pokemon is forced to alternate between that combo and cooldown for the duration of the encore.
Not an accurate, official ruling, but...
[BOX]10:18:31: <iar> You can Encore a Pokemon into a combo, right?
10:18:39: <Wobba> Yes
10:18:43: <Wobba> Iirc
10:19:19: <iar> other opinions?
10:20:08: <Wobba> Ask the ref
10:20:20: <EspyOwner> does Bug resist Poison in 5th gen
10:20:28: <iar> no, iirc
10:20:29: <Destiny_Warrior> hmm?
10:20:34: <Destiny_Warrior> encoring a combo was once ruled
10:20:37: <Destiny_Warrior> to be impossible
10:20:39: <Destiny_Warrior> iirc
10:20:46: <EspyOwner> it encores the last move in the combo
10:20:50: <EspyOwner> I thought
10:21:02: <Destiny_Warrior> you can't encore a combo as such, I know that much
10:21:12: <Wobba> Then ragnarokalex misinformed me
10:21:28: <Destiny_Warrior> he's clearly a misinformer[/BOX]
EDIT: I stand corrected...
[BOX]19:30 <IAR> Can you be encored into a combo
19:35 <Objection> yes IAR
19:35 <IAR> It was more directed at Alch... >_>
19:35 <Objection> you are then forced to alternate between that combo and cooldown for the duration of the encore
19:35 <Objection> oh
19:36 <IAR> It is one of those things that no one has an official ruling for as of yet
19:36 <IAR> well, a concrete one anyways
19:37 <Objection> pretty sure there was a ruling about it actually
19:37 <IAR> well if there is one
19:38 <IAR> it is obviously unwritten
19:38 Destiny_Warrior writes it
19:38 <Destiny_Warrior> there
19:39 <IAR> 6.6
19:45 <Alch> Lol
19:45 <Alch> Obrejection
19:45 <Alch> He is correc though.
19:46 <Alch> *correct[/BOX]