Making the change indicated should have no impact at all on the rest of the template ... not the look or feel, or the operation of it. If you noticed any alterations that occurred after you inserted that line then you must have done something incorrect when trying to either implement the template overrides, or in copying and pasting the code into place.
I suspect that the custom template you were using had some changes that were needed or made to the top portion of the site, and putting the html header in place may have caused those to be wiped out.
Do you have a link for the site?
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