That sounds like a bug.
I tried it here Handsontable example - JSFiddle - Code Playground
- Moved columns to get BAC
- Moved columns of the second table to CAB
Result : They remained the same after reloading the page.
I guess that other settings/options might be messing with the indexes. However, your solution sounds well. As long as you do not change the source data of the library the solution should be correct.