Daily (nightly) cron-driven patching does not sit well with LIDS. The only practical approach is to temporarily disable LIDS, patch and then immediately re-enable the system. The script below will does exactly this for a Debian system, but should NOT be used as is since it contains the LIDS password in plain text. Usage:
#!/bin/bash
#
# 1. Runs "apt-get update" and "apt-get --download-only upgrade" before
#    issuing "lidsadm -S -- -LIDS_GLOBAL", then "apt-get -u upgrade" and
#    finally "lidsadm -S -- +LIDS_GLOBAL", thus minimising the time
#    for which LIDS is disabled.  
#
# 2. Creates temporary expect scripts to temporarily disable and later
#    enable LIDS.
#
# -- update : ------------------------------------------------------------------
#
/usr/bin/apt-get update
    # ...writes to /var/cache/apt/pkgcache.bin
    #                             srcpkgcache.bin
# -- download : ----------------------------------------------------------------
#
/usr/bin/apt-get --download-only upgrade
    # ...writes to /var/cache/apt/archives/
# -- create expect script to enable LIDS : -------------------------------------
#
echo "#!/usr/bin/expect"                 >   /tmp/simonh.simonh
echo "  "                                >>  /tmp/simonh.simonh
echo "set timeout 5000  "                >>  /tmp/simonh.simonh
echo "  "                                >>  /tmp/simonh.simonh
echo "spawn lidsadm -S -- -LIDS_GLOBAL"  >>  /tmp/simonh.simonh
echo "expect \"password: \""             >>  /tmp/simonh.simonh
echo "send \"<password>\r\""             >>  /tmp/simonh.simonh
echo "expect \"changed.\""               >>  /tmp/simonh.simonh
echo "exit"                              >>  /tmp/simonh.simonh
# -- switch to "-LIDS_GLOBAL" : ------------------------------------------------
#
chmod 700 /tmp/simonh.simonh
/tmp/simonh.simonh
rm -f /tmp/simonh.simonh
# -- install : -----------------------------------------------------------------
#
/usr/bin/apt-get -y upgrade
# -- create expect script to disable LIDS : ------------------------------------
#
echo "#!/usr/bin/expect"                 >   /tmp/simonh.simonh
echo "  "                                >>  /tmp/simonh.simonh
echo "set timeout 5000  "                >>  /tmp/simonh.simonh
echo "  "                                >>  /tmp/simonh.simonh
echo "spawn lidsadm -S -- +LIDS_GLOBAL"  >>  /tmp/simonh.simonh
echo "expect \"password: \""             >>  /tmp/simonh.simonh
echo "send \"<password>\r\""             >>  /tmp/simonh.simonh
echo "expect \"changed.\""               >>  /tmp/simonh.simonh
echo "exit"                              >>  /tmp/simonh.simonh
# -- switch to "+LIDS_GLOBAL" : ------------------------------------------------
#
chmod 700 /tmp/simonh.simonh
/tmp/simonh.simonh
rm -f /tmp/simonh.simonh
 
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