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Aside from sound mix and colour timing changes, 'modernised' studio logos on new releases of older films are one of the revisions most likely to pop out and spoil the experience (for all their brief duration). The Bond movies are particularly disappointing in this regard, though most studios have been guilty of this trend at one time or other.
This guide details a method that I've found effective for simple logo replacements on Blu-ray titles. The advantage is that no reencoding of the main feature is required, so you maintain the full quality of the source; the downside is that it only offers a simple cut in video and audio, so it may not be suitable in cases where picture or sound continue across the transition.
You'll need:
The source Blu-ray for the feature you want to edit, an HD source for the original logo that you want to reinstate, TSMuxer and MultiAVCHD.
Part one: preparing the main feature
To begin with, you will need to make the necessary modifications to the main movie. The first step is to watch the opening of your movie and note the point at which the unwanted studio logo ends. I'll use WB's Mad Max 2 as an example: the current CG 'shield' logo has been added to the master, and fades to black at 17 seconds. You're going to perform a simple trim on the movie using TSMuxer, so you'll either need a rip of the disc ready on your hard drive or an unlocking tool such as AnyDVD that will let you work from the disc directly.
In either case, open TSMuxer and on the main 'Input' tab open the playlist for your main movie (using the playlist rather than the media files has the advantage of retaining the chapter points, plus it preserves the sequence of branched titles). On the list of streams, remove any that you don't want to keep - you may be taking this opportunity to add another audio track from elsewhere, so do that now.
Next, move to the 'General' tab where you will see the list of chapters. VERY IMPORTANT: you need to add a chapter mark to this list at the cut point you chose earlier - this will allow precise navigation to this point after the excess media has been removed. In my case I'm adding 00:00:17.000 to the chapter list.
Now move to the 'Split & Cut' tab. Tick the 'Enable cutting' checkbox and enter the time where you want your movie to start - I'm entering 17.00s.
Finally head for the 'Output' section at the bottom. Indicate that you'd like to make a Blu-ray disk, specify an output location and hit 'Start muxing'.
Part two: preparing the new logo
There are many ways to achieve this, but the main objective is to create a BDMV folder with the same audio/video characteristics as your main feature - this will ensure a smooth transition between the replaced logo and the movie itself. This may be as simple as finding another Blu-ray movie with the correct logo, and using TSMuxer's cutting tool to isolate that logo (in which case you'll be setting an End point rather than a Start point).
My preferred method is to use a video editor - Premiere Pro in my case - to trim and package the logo, including a clean fade to black and silence at the end. This method is particularly useful if you need to upscale another source, e.g. a DVD copy, to get the correct version. When you've done editing, export the video as 1080p AVC and the audio in the same format as your main movie (AC-3, PCM etc.), before using TSMuxer to package it as a (very short!) Blu-ray folder.
Part three: Combining the two parts
The best tool I've found for combining separate pieces of BD video into a semi-seamless sequence is MultiAVCHD's 'Merge playlists' function.
Start by opening MultiAVCHD and clicking the 'AVCHD / BDMV / DVD folders' button at the top. Browse for your replacement logo BD folder and open it (when asked if you want to switch to Blu-ray re-author mode, click 'No').
Next click the 'AVCHD / BDMV / DVD folders' button again and browse for your movie folder. Again say no to entering re-author mode.
You will now see the two parts you need in the compilation list. Click the 'merge playlists' button and specify a storage folder - this will create a combined playlist with all the necessary media.
One final step - convert this folder into proper BD format. To do so, click the big 'Start' button to the lower right and select 'Blu-ray disc'. This will copy your material to a folder in your default destination path (specified in the main window) - be sure to set this first.
Finally, test and burn your completed disc folder!
I hope this guide has been of some use - if anyone has any further questions feel free to let me know, and likewise if anyone can suggest any improvements to my method, I'd be pleased to hear from them.