I faced a similar problem with a music video. Multiple scenes trying to keep every thing lined up and some lip scync toward the end. Had a hell of a time trying to get it all to match up with the music- scene changes, action, and lip scync. As the audio was located in scene 1 I did not want to try to cut up the song and try to get it to play correctly over numberous scenes. since the audio disappears when you're working on a different scene it all becomes guesswork trying to estimate the number of frames required for every scene in order to come out where you need to be.
Then it accurred to me to use a line timer to solve the problem. Here is what I did and kept the scenes rather than moving at all to one timeline:
If you are using music in your animation, determine the beat of the audio. lets say in this case 14 frames per beat (Use an audio editor to determine beat rate.)
Make sure your frame rate in flash is the same as your audio in the audio editor. My case was 29.97 fps
Create a small graphic lets say a red square. Have it appear every 14 frames for a duration of 2 frames. Repeate pattern until you reach the end of the scene. Always
make sure you end the pattern with it one frame short of repeating the marker. The rest of your scene layer/s should fall somewhere within this last timing pattern. Don't worry if they are not lined up yet.
Begin new scene. Start your timing pattern at the first frame with a timing marker. Repeat #3, as per need. (Short cut: copy and paste timing layer using copy frames command by right clicking on layer. Note you will need to add 1 frame to the layer right after the first new timing mark per paste if your time line is longer than your intial paste & if you paste more than one time it will need to be done for each paste.) Saves a ton of time.
5 Remove extra timing marks. End as you would in #3.
6 Here is the tricky part and requirews a little thinking, but this will line every thing up and get it to run to the beat. Add or remove frames in the rest of your layers to the end of your marker frames but just before a new timeing marker appears. in other words if your final timing marker in the scene is only 4 frames from the end of your current layer subtract the frames so the layer ends before the last timeing marker. so you now at some point need to add these frames back in. You may be able to do this in the next scene. The way to keep track of this:
formula for tracking:
1. A# = added number of frames;
2. R# = removed number of frames;
3. NA# = need to add number of frames;
4. NR# = need to remove number of frames;
Sample of how it gets used:
1. N0 Scene 1 R4 NA4;
2. NA4 Scene 2 A6 NR2;
3. NR2 Scene 3 R10 NA8;
4. NA8 Scene 4 A8 NR0;
Okay here is the logic behind this chart. Starting at the begining of frame 1 scene 1 you are at 0 (N0)**You do not need to add frames to the beginning of this scene. If you remove 4 frames to get to where you need to be in association with your timing marks(R4)** Then you need to add them back in (NA4). Carry over the NA4 to the next line on the chart or scene (NA4 Scene 2). next you had to add 6 frames in scene 2 (A6) since you already needed to add 4 frames and you added 2 more than what you needed you now need to subract these 2 extra frames at some point Need to Remove 2 frames (NR2)
hence (NA4 Scene 2 A6 NR2)
NR2 Scene 3 R10 NA8 Needed to remove 2 frames in scene 3, you removed 10 frames you now need to add 8 frames back in.
NA8 Scene 4 A8 NR0 needed to add 8 frames in scene 4, you added 8 frames which just happens to end at the right spot on the timing marker layer. Now everything is synced up you can add additional scenes making sure that you end your scene as described in number 3 of these instructions. Everything should sync up perfectly. If you have any problems you may have to adjust one or two frames either direction in previous scenes to make up for the lag that flash has.
you always want to get back to a 0 point or (N0)
Also now that the time markers are blinking during your animation you can also add lineup/sync other animations that occur within the scene to the beat of the music.