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After updating to ver.6, do I have to set cue points and beatgrid for my tracks again?

No, you don't have to set them again.
When you run ver. 6 for the first time, your current library will be converted for use with ver. 6.
All information in your library, such as cues, beatgrid, and playlists, will be copied over. (Alternatively you can select [File] > [Library] > [Import your library from ver.5 (or earlier)].)
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