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I started a partial extract recipe (Belgian Dobbel Dobbel) from Noble Grape the other day. This is also the first time I use liquid yeast.
I just moved the everything to the secondary fermenter after 4 days in the primary after the yeast cake finally dropped. During the few times I lifted the primary fermenter lid to check the yeast cake, I noticed a strong apple smell and after moving the beer to the secondary fermenter wort tasted quite sour.

Now I'm reading that it could be normal in higher gravity beers and that moving it to the secondary fermenter at this stage could actually ruin the beer.
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I was following pretty generic partial extract instructions that said to move the wort after the yeast cake drops after 2-3 days and it stated that it can be "hazardous" to the beer if it sits more than 5 days.

Should I have kept the beer in the primary fermenter for longer till the sour taste is gone? I've been always been very paranoid about contamination, that's why I never thought of taking a sample during primary fermentation. How would I have known when to move it?

Should I move everything back to the primary fermenter or is my batch ruined?
EDIT: I already cleaned the primary fermenter and threw out the yeast/hops sediment that would be necessary to 'clean' the sour taste out.

I definitely wouldn't have moved it that quickly. I usually let it sit on the yeast cake for around 3 weeks before I secondary, if I even bother racking it at all. Don't worry about the apple smell its just acetaldyhyde from fermentation, just give it time and it should clear up as there is still plenty of yeast in your beer to take care of it.

I have a friend who did that beer and I was shocked that his NG instructions told him to rack it in 4 days. He said his turned out okay though.

Those generic instructions NG give with their kits are pretty bad.

yeah i would say leave it in your seconday for longer than the instruction say, and let yeast in suspension clean it up. try to find somewhere with a good stable temperature too, i find that really helps the yeast to do their job.

A year ago I racked my first batch to secondary when the krausen fell after three days as per Noble Grape's instruction sheet. A second krausen formed with no head-space in the carboy, and foam started spewing out through the airlock. I had to use a blow-off tube on my secondary fermenter! The beer turned out fine.

You're better off to just recycle NG's instructions.

You can easily go 3 weeks in the primary from my experience. Those instructions are horrid.

Don't put it back in the primary, it's not necessary and the extra mucking around with it will aerate the wort (can be bad at this stage) and introduce infection. Best to just leave it alone in the secondary until it finishes. A lot of folks use only one stage (start in carboy) and let the krausen foam blow off through a large diameter tube for the visibly active phase of fermentation. This avoids the transfer step and lessens the infection risk and makes it easier for lazy brewers like me. After the active krausen step, you'd attach an airlock to let it finish. As for the sour and apple taste, you are tasting it mid-ferment, so there are a lot of flavours present that will not be there when it's finished. As Ladd said above, apple is acetaldehyde which is produced by the yeast during fermentation and which they re-absorb at the end of fermentation. As long as you don't crash cool the yeast into dormancy prior to the end of fermentation the apple smell will go away. Sour is normal too. It's good to taste what's going on throughout the process though so you understand it better. Now all you need is patience to let the beer finish and drop out clear prior to bottling or kegging.

Thanks for the advice everyone! I'll just let it sit for a couple weeks, hoping for the best. Looks like I'm going to have to be patient with this one as there's less yeast left in the wort.