Brackets [##] after the
series name in the series column is just a display of
{series_index} << the field name that was visually merged. That is fixed.
A value of [1] is the result of
setting the Series, but not the Index
BTW if typing in the GUI you do type [#] after the name. Calibre parses that to the proper place in the DB. You can not use anything except digits and a period. Fractional ending in 0 are also not doable (2.50) will always show as 2.5
Manage Series Plugin helps you
order (number) selected books