.htaccess on a double WordPress multisite installation

I have a problem I can’t find the solution on and hope somebody are willing to help me.
I have have two multisite wordpress installations on the same server – one is the live site (http://xx.se) and the other is the development site (http://xx.se/wp). When development is stable I transfer it to the live site.
However now when I have done it for the first time it appears that the .htaccess file is changed by the wordpress installation of the live site (I did run joomla there before and then it didn’t affect). The live site is working nicely but I can’t connect to the development site without copying back the old .htaccess file. What I like is that both separated multisites wp installations can be used at the same time. Anybody knows how to set up the .htaccess for this? I tried the tip from this thread but it didn’t solve my issues .htaccess rewrite WordPress Multisite

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