I’ve had this issue of the sequencer file getting confused and rendering the wrong thing, but I think it’s because I was doing things wrong. I know this was a couple of years back but it might help someone.
To create a new copy of the sequence do the following -
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In the sequencer window, click the spanner icon at the top and select ‘save as’ and choose a new name (DO NOT duplicate it and rename it, I think this confuses the engine, it probably gets the copy mixed up with the original which is why it will render the assets referenced to the older level if you saved it as a new version)
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In the project outliner on the right hand side, search for ‘sequence’ to select the NewLevelSequence asset. In the details panel for the ‘NewLevelSequence’, under general, change the level sequence asset to the new sequence. This will ensure the level uses the new sequence and not the old one.
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Save the project.
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When rendering, select the render task in the queue and check on the right hand side that the correct level and sequence are selected to be rendered.
This shouldn’t give you any issues.
If you do have a mixed up sequencer that seems to render the wrong thing try saving it as a new version first using ‘save as’ as mentioned above, if this still doesn’t work you can try right clicking on the asset in the sequencer and select ‘convert to spawnable’, this has worked for me in the past. If you need to change it back, you right click again and select ‘convert to possessable’. Just be aware that spawnable assets will only load when the sequencer is loaded. Basically spawnable means that they are loaded by the sequencer and possessable means they are loaded by the level.
If all assets were set to spawnable then you could probably use ‘save as’ without having to reassign everything in the sequencer, as they now belong to the sequencer and not the level. I’ve not tried this myself but in theory it should work. Though if the sequencer got corrupted you might lose everything that was spawned by it in the level! Be sure to keep backups!
Another issue that newcomers have is that the camera cuts track doesn’t have the correct camera on it. So the render will come out wrong. On the camera cuts track, click the + symbol and select ‘new binding’ and select the camera, then move it into position on the timeline.
Hope this helps someone, as I could have really done with this info myself but just couldn’t find it anywhere! As I slowly learned my way around and found all the options, I eventually figured it out.