One thing that's
SUPER CONFUSING is that your logs are in reverse chronological order. Not sure how that happened but it took me a while to realize that. So the order of events isn't in the standard order.
So, if you put them into the correct chronological order, at least one pattern more easily emerges:
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2018-02-07 16:42:19.645 Action Collection Error insert timestamp into variable action references variable that no longer exists
2018-02-07 16:42:19.646 Action Collection Error insert timestamp into variable action references variable that no longer exists
2018-02-07 16:42:19.647 Action Collection Error insert timestamp into variable action references variable that no longer exists
2018-02-07 16:42:19.648 SQL Logger Debug (u'04:41',)
2018-02-07 16:42:19.648 SQL Logger Debug INSERT INTO variable_history_136602142 (value) VALUES (?);
The first 3 lines are errors that indicate that there's an
Insert Timestamp into Variable action somewhere (action group, trigger, schedule, somewhere) that's trying to stuff a timestamp into a variable that no longer exists. These seem to come in 3's, and they look to be happening about every 90 seconds, which leads me to believe that they're in a schedule. The next two SQL Logger lines seem to indicate that there is at least one more insert timestamp action that is successfully completing, and that the change is getting logged by the SQL Logger plugin.
There is also another pattern which may or may not be indicating something else. My spider sense is telling me that it's not related to the above, but rather just happening on a schedule that's very similar to the one which is causing the issue above. But there are examples of times where they aren't exactly in sync so I think they may be two different schedules. Here are the lines:
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2018-02-07 16:58:42.960 NEST Home 2 Setting up the API...
2018-02-07 16:58:42.961 NEST Home 2 Refreshing NEST map from home.nest.com...
2018-02-07 16:58:42.962 WebServer Indigo Touch client connected from 192.168.1.6
2018-02-07 16:58:42.963 WebServer Indigo Touch client connected from 192.168.1.27
2018-02-07 16:58:42.964 WebServer Indigo Touch client connected from 192.168.1.6
You always see those two NEST home lines followed immediately by at least 2 and as many as 6 occurrences of Indigo Touch (re)connects. IMO, that's too regular to be coincidence. I'd be curious to hear what happens if you disable the NEST thermostat but change nothing else from what was on during this log snippet time. If the Indigo Touch connection messages go away when the NEST Home plugin is disabled that would seem to be a firm correlation.