[Gautam Pandey]"Is there a way to have TC in the clip when outputting from AE?"
What version of AE are you using? AE CS5 adds a timecode track to rendered MOVs.
If an upgrade is not feasible, here are two other ways you (or your editor) can fix the timecode problem. It's very simple to do in FCP, but if you don't have FCP, or if you're on Windows, you could buy the cross-platform QtChange utility from VideoToolShed.
Import the clip that lacks timecode. Select it in the browser, then click Modify > Timecode. Tick the "Source TC" checkbox and set the starting timecode to whatever value you require.
This is one of the few changes that FCP will make destructively; in other words, this will actually alter the original file when you click Ok. In this case, it will add a timecode track. To test, you can remove the file from your project and re-import it. The timecode will now be correct.
In Finder or Explorer, create a folder which will hold your non-timecode MOV (and only that one file), and move your file within that folder.
In qtChange, under Select Input, click "Pick source folder" and choose the folder that contains your MOV. Under Add / change TC / rename, enter the new starting TC and click the "add / change TC track" (it will turn green). Finally, under Reset or Alter, click "Alter all clips!"
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