The txt store-output from Qlik will have UTF8 as fileformat and AFAIK it's not changeable. But there are various tools available, for example notepad++ which could convert such file-formattings and probably there are also some which could be automated in some way. Even vbs-macros should be possible like this one: Re: Ansi codification.
I assume that this question is related to What is the difference between 2 stored csv files? Page encoding and I could imagine that you could convert it on the MS SQL Server side by not inserting the data directly else by loading them into an extra table and then using a query on this table to convert the critical fields and inserting it into your target-table.