I need major assistance from Logic Pro users. I have a project with a vocal track and some punch-ins just like any other person would have. Normally when you select a take it replaces that section with the take….well for some reason when I click the take it puts in that take but it gets rid of the whole rest of the track as if it was silence. Did I accidentally do something with merge/comps/etc?
I work with logic almost everyday and I still couldn't understand what you're doing and what your problem is.

Would you mind trying to explain that a bit more clearly?
Name's Luca.

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When you say 'section' do you mean you have the various bits of the track chopped up into regions? If so, comped regions should not affect the whole track, try looking in preferences to see if you have some strange setting for comped tracks to respond that way (haven't seen one, but I'm using Logic Pro 9 still... if you're on X, might be why).

If they're not chopped into separate regions, that would be why and you need to either chop them into separate regions, or highlight (by click-dragging over) the area you want to be part of the comp.

My only other idea is maybe you've just clicked the track header (down left hand side, where you can mute/solo/record arm etc. in arrange window) and it has selected all regions in the track (does this by default) and you're changing a take which is for some reason replacing all regions? I don't know if/think Logic would do this, but just a long shot. If so, make sure you select individual regions instead by clicking on to a bit of blank space in the arrange window, and then clicking on the region you want to change rather than just the track header.
Hey, look. Sigs are back.
I don't understand why nobody is getting my questions (on here and elsewhere). Okay so I had the vocalist go through the entire song. We then went back and punched in to fix parts of the song. So I have one full audio file with a bunch of different punched in takes in the take folder. When I drop down the take folder and select a small take (ie one line of a verse,etc) it inserts that punch in however the rest of the normal file (the 1st track) turns into silence. When I do this the 1st original track is shown grayed out at the bottom of the take folder.
Because you aren't explaining it very well/with much detail. By the sounds of your latest post, it's possible that by clicking the punched-in region in the take folder, you're clicking to replace the whole region (because you haven't separated the track into regions, the region is the entire track).

Just try this, instead of clicking that area drag/highlight the punched take you want to put in the comp track. Literally just click (and hold) where you want to begin replacing with the punched take, and then drag across the waveform until you get to the end of where you want to punch in with, and then release the mouse button.

If that doesn't work, we need screenshots and more detailed info etc.
Hey, look. Sigs are back.
Sounds like a coming issue, the new punch in is probably on a second level which gets selected thus bumping down your other take.
Haven't used Logic recently but in Sonar and Studio one the way you do it is by highlighting the bits that you want to use from the pieces of takes, then they show up in the master comp track.

Lookup vocal comping in the manual, maybe these lessons will help: