OK, there’s two issues there:
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It seems your Data2 raw data was converted outside of MRtrix3? There’s not a lot we can do to fix invalid input data… If this was DICOM format, I’d be willing to look into it, since we take great care to ensure the conversion works as expected for all major manufacturers. But as soon as it’s been converted, it’s pretty much impossible to ensure any subsequent correction actually does the right thing. I strongly recommend starting again from the raw DICOM of you can possibly get access to it.
In your case, it does look like inverting the Y might be sufficient, but it’s not guaranteed if the data are potentially acquired in an oblique orientation. Maybe you can use @bjeurissen’s dwigradcheck and see what that tells you.
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for your Data1 case, the main thing is to never transform FOD data (or DWI data in general). These images contain orientation information, and the relationship that information relative to the orientation of the anatomy or scanner will be affected if you reorient the images. Dealing with this requires dedicated handling of the information in the images. Basically, the simplest thing to do to avoid issues is to never transform any DWI or derived data, unless you know the tool you’re using to do this is designed to handle this exact type of data (most won’t). Already register the T1 to the DWI, never the other way round…