I have backported the (temporary?) fix from bluez CVS to Ubuntu's bluez-
utils 3.26-0ubuntu6 package that makes the IO timeout for input devices
configurable via a conf file, including the default option of having no
IO timeout.  Attached is the diff of the package source.

I have tested it (using Gnome) and having no IO timeout for input
devices appears to have solved the problem for me.  However, I do not
know what long-term effects, if any, this will have on things like mouse
battery life, etc.  Removal of IO timeouts for input devices may have
other effects that I have not forseen.  (I don't really understand why
there was an IO timeout for input devices to begin with...)  Also, I use
a desktop computer, so I don't know what effects, if any, it has for
laptop and other battery-powered computers.

Assuming you know how to build Debian/Ubuntu packages from source, you
should only have to get the build-dep and source for the bluez-utils
package and use the following commands:

patch -p0 <bluez-utils-3.26__input__.diff

The patch should apply with no errors or warnings.  Then you need to:

cd bluez-utils-3.26
aclocal
automake

All should then be ready to build the package.

To experiment with the IO timeout, copy input/input.conf to
/etc/bluetooth/input.conf and change the IdleTimeout parameter to
however many minutes you want.  No conf file, or a commented-out
setting, means no IO timeout for input devices.

Based on the link in comment 9, it seems that bluez developers might
work to find a better long-term solution that correctly disconnects all
input devices when they timeout.  However, this patch is here right now,
and it seems to fix this problem without breaking anything else.

** Attachment added: "backport of bluez utils CVS changeset to remove IO 
timeouts for input devices"
   http://launchpadlibrarian.net/14659037/bluez-utils-3.26__input__.diff

-- 
Bluetooth Mouse looses connection after some time of inactivity
https://bugs.launchpad.net/bugs/175743
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