I spent all day processing a huge 2500 frame timelapse, only to realise when watching the final video that there were many frames missing.

Indeed, the RAW files were not present on my PC, but they were on my camera still.
I originally imported them with Lightroom. Perhaps this wouldn't have happened with the LRT import.
I tried to import the missing ones, but Lightroom said they are all there and that the missing ones are all 'suspected duplicates'.

The filenames are the same as others I have in the catalogue, because I take about 2000 per day, so the numbers repeat often.
The EXIF data would be similar but not identical. The Date/Time would be different, though the lens/body would be the same.
So I don't really know why it thinks they are duplicates, especially when they're going in a different folder.

Anyway, I don't really know what the workflow is now. Manually hunting for missing files would be incredibly time-consuming. And if I do manage to import all the missing photos, I wouldn't know how to maintain my current color grades/keyframes without breaking things.

Would it be possible to check for filenames with non-consecutive (when I have thousands of them)?
Is there a way I can avoid doing this in the future?
How do I insert the missing frames into my project without things breaking?

Thanks!

That's why LRTimport (the importer in LRTimelapse) is the recommended way to go. It renames files with timestamps, merges the different folders on the memory card etc. In order to avoid such issues.
If I were you, I'd remove everything from that shooting from lightroom, delete the folders on the Hard-drive and start over importing from the memory card via LRTimport.

This worked great. As usual, your application has a far superior workflow to Lightroom. I'll be sure to do this from now on.
Thanks so much for your continued hard work.

Glad this is working for you now, thought so! :-)