Investment accounts are somewhat different to all other account types in Moneydance, they work in an entirely different way.
In my experience for Investment Accounts, Batch Change --> Category impacts the 'Transfer' field not the category field.
I suspect there are a couple of factors at work here, firstly 'Category' is used for both what are definition of Income or expense and secondly it can also be used to give a transfer account. This is seen in QIF files where the same field descripter is used and also in all the other register types where the one field is used for both purposes, only in Investment accounts are there two fields.
Also Investment accounts make use of combination transactions i.e. there are two transactions shown as one, which I think may confuse things.
I do not think that Batch Change has the smarts to deal with some of the unique features of the Investment register.
I think the category is the category to assign any seller or buyer fees to. If there is no fee then that item is greyed out and unused. There is no batch change for transfer destinations. I guess this is a feature request.