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However, the fact that the two dialogs share the same checkbox is a bug. I have fixed it, which should go a long way toward solving your problem.
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This is precisely what I was hoping for
Thank you!
Regarding the first issue, Do you guys plan on adding in a option so we can re-enable the warning without loosing all that customization data?
In the meantime, will deleting the .pickle file you mentioned loose any non-cosmetic data? I don't really care about column sizes and orders, but I'm curious if anything in that "bunch of other things" you mentioned isn't cosmetic, such as any form of book metadata, or even the per-book conversions settings, and things of that sort.