'Over two weeks' can have two different meanings, depending on context. It can be 'more than two weeks', or it can be 'spread out for the whole two weeks'.
'It has been over two weeks since I have had any mail' vs 'Can we minimise disruption if we do the work over two weeks?'.
'in over two weeks' would be the 'more than' context. Something has not happened for more than two weeks.
'for over two weeks' has both 'more than' and 'spread out'. it has the sense of something has continued to happen for that long. 'I have had a cold for over two weeks'.