Repair is fine - all the data seem to be in SSTables. I've checked it and while index tells me that I have 1 tombstone and 0 live cells for a key, I can _see_, thanks to sstable2json, that I have 3 "live cells" (assuming a cell is an entry in SSTable) and 0 tombstones. After being confused for the most of the day, now I'm almost sure it's a problem with index (re)building.
I'm glad to hear that. I feared my ticket might be responsible for your data loss. I could not live the guilt ;-) Seriously: I'm glad we can rule out the repair change.

The same: for key-based query it returns correct result no matter if I use CL=ONE or TWO (or stronger). When querying by indexed column it works for CL=TWO or more, but returns no data for CL=ONE.
Yes, if it works with CL=one, then it must be the index. Check the mailing-list, I think someone else posted something similar the other day.