I used Avidemux several times to rotate videos that I captured with the camera mounted vertically, because of the use of 1080p resolution.
However: Avidemux takes ages to rotate them. I had to change the video output, in order to rotate the videos.
Why this is happening?
If the camera stores videos as mp4 and you don't want to change the container so that the only problem is rotate flag not set correctly, you can set rotation in the configuration of the MP4 muxer in Avidemux without re-encoding the video. You need a recent build (https://avidemux.org/nightly/) for that (2.7.2 nightlies are almost identical with the upcoming 2.7.2 Beta release, due very soon).
If you re-encode, the choice of the codec, its settings and the hardware used to run Avidemux determine how long it takes. If you have a recent NVIDIA graphics card and speed matters more than quality or compression rate, you could use the "Nvidia H264" (or even HEVC, if the target equipment supports HEVC) hardware accelerated encoder, which is blazingly fast at high bitrates.