Picard CleanSam does not actually remove any reads from the SAM file.
Here is what it does: "Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads"
All it does it ADD soft clips to reads that go over the edge accidently.
I have tested this and it seems to be true. No reads are removed.