Quite a regular 
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If the script for auto-installing is correctly written and makes use of the proper way to update *all* files on the file system (do not remember the name of the dedicated shell command atm) then you should be able to browse all your installs in the rollback utility and find the one that updated both libs, rollback this one and AmiUpdate will offer you the ability to download again the package.
As Joerg said libc.a should not be in the same update as newlib because they are targeted to different audiences: users VS developers. There is different situations where mixing won't work, you named one, but what about when I install the update as a simple user (so no SDK installed, hence no place to install the libc.a) but later on I learn how to code and install the SDK? I advise making two updates one for newlib and one for libc.a the second requiring a given version of newlib (can be described in AmiUpdate database) BTW AmiUpdate also checks using filesystem dates as a last resort.
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