Is there a way to rebuild indices for all the classes in a given namespace?

There is no such command.  I would recommend moving the index global as well.  However, if this is not an option then you probably want to do something like:

USER>s sql="select Name from %Dictionary.CompiledClass where system=0 and NOT(Name %Startswith '%') AND SUPER [ 'Persistent'"     


USER>s rs=##class(%SQL.Statement).%ExecDirect(,sql)                                                                               

USER>while rs.%Next() { s sc= $classmethod(rs.%GetData(1),"%BuildIndices") w "Built "_rs.%GetData(1)_" with return code = "_sc,! }

Obviously this is kind of hacked together and you'll want to clean it up, but the outline is there.  I had to make some assumptions like you don't have any other classes in your application that have 'Persistent' in them.  If you do then you'll want (Super [ '%Library.Persistent' OR Super [ '%Persistent').  Since classes are case sensitive this should be fine.