@m0d : thanks for the in-depth analysis. Will be useful to correct the issue you reported.
Two things I noticed, though.
Manually creating file allows the import of the entry. But, in one case I had to delete it in order to resume download, (YTD does not handle existence of file due to the fact that it already renames it (to .download), therefore it expects it not to be there).
Also, it might be better to just handle Queue as in progress after all - do not back up until queued are completed. As some of the downloads that were in Queued state already started earlier. But, after I imported them it resumed wrong, (did not MUX in some cases). Which means that it did not check the exact point of where the download was, i.e. downloading video / audio / or MUX .
It might have took longer, but I was able to add the files back to dashboard. In the end Queued states are better off handled as in progress since they require some work to be completely compatible, (or just import them and delete all already downloaded files (.mpg temp and .m4a temp files) to Force redownload to make sure it downloads properly).