I'm looking for a program, that can replace low-quality audio track in video with high-quality one from lossless audio file. It also must be available to shift HQ-track position. I want to do these operations at least with MP4-files. I use Windows 7 64-bit.
You might want to look at VirtualDub.
From its list of video editing features
- Reads and writes AVI2 (OpenDML) and multi-segment AVI clips.
- Integrated MPEG-1 and Motion-JPEG decoders.
- Remove and replace audio tracks without touching the video.
- Extensive video filter set, including blur, sharpen, emboss, smooth, 3x3 convolution, flip, resize rotate, brightness/contrast, levels, deinterlace, and threshold.
- Bilinear and bicubic resampling -- no blocky resizes or rotates here.
- Decompress and recompress both audio and video.
- Remove segments of a video clip and save the rest, without recompressing.
- Adjust frame rate, decimate frames, and 3:2 pulldown removal.
- Preview the results, with live audio.
FFMPEG is able to add and replace audio (and video, subtitle, etc) tracks in files without re-encoding.