SYMPTOM
Statistics logging enabled for some (or all) project in the metadata are found reset to blank after Intelligence Server is configured again with the same server definition selected in Configuration Wizard.
Before Intelligence Server re-configured:

After Intelligence Server re-configured:

CAUSE
The option to enable statistics is unchecked while running Configuration Wizard. The checkbox is for "Make this my default Statistics Database Instance for the local Intelligence Server metadata."

When this checkbox is unchecked:
All of the projects where statistics logging already enabled with a custom Database Instance will be reset to none.
When this checkbox is checked:
Either a new Database Instance called "Statistics" will be created or an existing Database Instance called "Statistics" will be updated with a new DB Connection that you specify via Configuration Wizard, then, assigned to the projects where Database Instance was not selected for statistics logging.
On the other hand, if the project(s) already have a custom DB Instance specified for statistics logging such as shown in the first screenshot of this article, then, the setting will NOT be overwritten.
ACTION
Since there is no option not to enable statistics for the projects that do not need statistics logging enabled while keeping the existing setting for the rest of projects as they are, proceed with either option -- check or uncheck the option, then, make necessary adjustment by going back to Project Configuration > Database Instances >Statistics.
Alternatively, Command Manager can be used to re-enable statistics logging for the projects. For example,
ALTER STATISTICS DBINSTANCE "Statistics" BASICSTATS ENABLED IN PROJECT "Strategy Tutorial";
For additional options, refer to:
Alter Server Configuration statement
Automating Administrative Tasks with Command Manager
KB440873