Word which encompasses both "logs" and "notes"

You may consider journal:

A journal is a location of stored activities or events occurring on a computer or network.

A log entry would be an event. But this is not a term that can be used for notes very well. However perhaps the nicely ambiguous term annotation can serve?

A note by way of explanation or comment added to a text or diagram:
marginal annotations

References:
http://www.oxforddictionaries.com/definition/english/annotation
https://en.wikipedia.org/wiki/Annotation

History

http://www.merriam-webster.com/dictionary/history

During our last project "history" is what we named a similar collection of chronological system generated logs and user generated comments.

We referred to the individual instances as a "history item" or "history record"

Diary (TFD):

• A daily record of events or measurable phenomena, usually kept to track patterns over time: kept a diary of blood sugar levels.
• A book or computer file used for keeping such a record.

The term has been used to record "sessions" in softwares like Matlab (write to a diary file) or Octave (Help to Log, Save and Edit).

In the context of Information Technology, specifically the nomenclature we use for our Salesforce Database, we use the term Documentation

The usually printed instructions, comments, and information for using a particular piece or system of computer software or hardware

Source: Merriam Webster

We use "documentation" as a catch-all term for the automated logs generated by the various moving parts of the system as well as the manual system changes and notes added by our administrators. When we need to refer to a single part of the documentation, we call it an entry.

Hopefully this is helpful.