Those paths are unfilled with a black stroke?
Can you try and outline them?
Thanks for the suggestion. Outlining didn't work either. The only way I've found to make it save right is to rasterize the dissapearing paths. Not the best solution since it makes curved lines look blocky, but it'll work for this logo, anyway.
That being said, I'm open to ways that don't involve rasterization if you (or anyonw else) can think of any.
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I think what was meant by outlining is to convert the stroked paths to objects... Menu: Object > Path > Outline Stroke
Personally, leaving strokes in logo assets can be dangerous because you never know if someone down the line will open it, scale things (for whatever reason) but forget to consider scaling the width of the stroke as well. Best convert them to shapes when you're finished your design (keep a working file with the strokes intact, of course)
Thanks. This helps a lot. I think I've got the problem figured out now. I appreciate your advice!
I noticed that if you have some objects grouped, they're disappear or radically displace themselves. If anything spontaneously misaligns or disappears, try to ungroup everything.