Yeah, I don’t think it’ll work on samples that are longer than the pattern lengths — I usually work with drum loops that are only 2-4 bars long. One hard part might be highlighting across multiple patterns and i don’t think that’s supported. I know there’s “Autoseek” where a sample can span across more than one pattern, but I think that’s for playback only — not sure if you can render to sample without doing a full-blown render of the project.
I think the max pattern length is 512 lines and you can change you number of lines per beat (LPB), so maybe you can have a separate Renoise session with long patterns just for converting these samples… Of course, this isn’t unlimited, so you might still run into cases where it doesn’t fit.
How about you just cut your original samples into chunks that fit in your pattern length? Isn’t the goal to slice them anyway?
Personally I wish I could find some command line utility for timestretching/beat sync, so I could write quick scripts to process these things in batches, but this is totally off topic