I am able to reproduce this issue consistently in a distributed CDAP, but not at all able to reproduce it in SDK.
1) Have an IndexedTable and index on column 'c'.
2) Write a row with key 'key1', column 'c', and value 'v'
3) IndexedTable#readByIndex('v') will return the recently written row, as expected
4) Write another column (for example 'd') to the same row 'key1'). This other column must not be one of the indexed columns.
5) Step 3 should still work, but it doesn't. IndexedTable#readByIndex('v') returns zero rows.