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The addon programs have no impact on the Kobo firmware updates. The firmware updates can overwrite the launcher program (The Kobo Start Menu (KSM8), Advboot, or the File Monitor (fmon)), hooks into the startup code. You can avoid that in the case of KSM8. Reinstalling the other launchers after a firmware update should also work. The alternative reading programs themselves are run in their own code space and are not likely to be effected by Firmware changes.
Both KOReader and Coolreader have OPDS support, so they can easily access calibre's wireless content server. KOReader also can connect to calibre as a wireless device.
Luck;
Ken
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