what should I do if I get a compromised sample of scRNA-seq data?
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The knee plot is just one type of QC. I'd say just proceed with your analysis and see if you observe anything funky (analysis itself is a QC). You should also see if you can use a tool that removes doublets and ambient RNA, if that helps your analysis.
Agreed. I would just force the cells to 5000 or so, and then proceed with the normal QC. If there's a lot of trash "cells" in the dataset this will manifest by poor QC metrics such as number of detected genes and mitochondrial expression percentage (since mt genes usually are highly-expressed so they're always detected first), plus "trash" tends (in my experience) to cluster together with marker genes that make no biological sense. Just try a bit, see what works.