Opening a file from an older/newer version change warnings seems to be broken. I consistently get these warnings from 1146 when opening fonts compiled with 1146.
It doesn’t mean it’s broken. If you have components that use anchors or have disabled alignment, then export to TrueType. When you open such a file, the extra information is gone and the alignment will produce a totally different result.
I am having the same problem. I just saved a Glyphs file yesterday, in version 1149. I opened it today after updating to 1150 and I got the warning message. No changes were done in the meantime.
It is not a big issue in this specific case, but I am getting this warnings in files in which no changes concerning components were done. I am also worried about those changes (displayed in yellow) concerning width values!
Can you send me this file (as it was saved in 1146)?
I had a look at the file. I can trigger the dialog in 1149 when editing the version number in the .glyphs file. I think the problem is that there are some nested automatic alignments. So you need to align it a few times until it settles.