I don't think there's any hard feelings between the two of them. Sheff withdrew from Shearwater because it no longer needed him, if you will, and Meiburg did the same. When I saw Shearwater back in May I talked to Jonathan, Kim, and Jordan after the show and all three, independent of the others, told me that the split was completely friendly.
The important thing is that each band is better than ever. This is all I care about.