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^ I reinstalled grub2 and os-prober, and it didn't re-enable the exec bit.
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OK, I am slightly surprised but also clearly wrong. Sorry about that.
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dpkg respects files under /etc (or any file marked as a conffile) as being the province of the sysadmin, and never undoes sysadmin edits without permission. (It uses (md5?) digest sums to keep track.)
My understanding, after package upgrade, three cases:
1) Package wants to change file, sysadmin has not edited file: package change is implemented.
2) Package does not change file, sysadmin has edited it: sysadmin edit remains.
3) Package wants to change file, sysadmin has edited it: dpkg puts up a dialogue asking what sysadmin wants to do.
This is why reinstalling a package is not enough to get /etc/* files back to the default state - you have to purge, or otherwise make sure no conffiles remain on the system.
Also, this is only for conffiles - files under /usr/share or wherever are just overwritten in an upgrade.
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^ Useful info, thanks
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