We can't know. We do not know anything about your project, in particular what keyframing you used on the time-rremapping/ timewarp. You are losing yourself in vague descriptions of the blue sky...
You need to read up on time remapping. For example: you have a 30 second clip shot at 30 fps and you want to play a clip at normal speed for the first 10 seconds, then, and heres the hard part to wrap your head around, slow down the next 10 seconds to 1/4 speed to simulate shooting the clip at 120 fps, then play the last 10 seconds at normal speed. The hard part to wrap your head around when you do this is that the middle 10 seconds will now take 40 seconds to playback.
Here's what you do:
- Enable time remapping
- Note that there are 2 keyframes, one at the first frame and one that is 1 frame past the end of the video (I won't explain why it is there but trust me it makes sense)
- Move your CTI to the 10 second mark and set a new keyframe by clicking the diamond in the Keys column in the timeline
- Move the CTI to the 20 second mark and set a new keyframe
- Extend the length of the composition to one minute and ten seconds (this is some of the hard part to wrap your head around)
- Move the CTI to the end of the extended composition and set a new out point for your video by pressing Alt/Option + ]
- Now move the CTI to the one minute mark (one minute because the middle 10 seconds is now 40 seconds long so the end of the slow mo section will move from 20 seconds to 1 minute
- Select the last two keyframes and drag them to the left until the keyframe originally set at 20 seconds snaps to the one minute mark and the last keyframe is one frame past the out point of the clip
That's all there is to it. Your new modified video plays at normal speed for the first 10 seconds, 1/4 speed for the next 40 seconds, then resumes normal speed. You can check out the speed graph to verify the speed change and even modify the curves so the change in speed is smoothed out, but if you do that you should have decided before you moved the last two keyframes and set two additional keyframes at san 10:10 and 19:20 to give you a few frames to ramp up and ramp down your slow mo.
The thought process is the same no matter what technique you use to change the speed in the middle of a clip. If you want to return to normal speed after the speed change you need to define the outpoint of the speed change and move the outpoint and the end point of the speed change down the timeline for slowing down a clip or up the timeline for speeding one up to return the clip to normal speed.
Now all you are stuck with is how to make the slow motion segment look smooth because you are repeating four frames at a time. Twitter is probably the best tool for this but it is expensive. AE's frame blending does a fairly good job on most video. Some video will not successfully slow down more than 1/4 speed no matter what software you use. Some video will slow down to 1/10 speed just fine using nothing more than Time Remapping. It all depends on the shot.
I'm certainly no expert on AFX but I always add the time warp effect to an adjustment layer instead of the camera video, it seems to make the total length of the clip / sequence more predictable.