How to restart Google App Engine Standard Service
It's likely good practice to cache your dataset as you're doing; if you know the data hasn't changed. then there's no need to requery BigQuery for it.
However, your dataset does change, just once per day.
So, I think your approach should be to revise your app so that it refreshes the cached copy of your BigQuery dataset every day and stop|block your users from querying the dataset as it changes.
You actually need only change the dataset if a user requests it (there's no need to refresh the dataset on days when no users need it), so, depending on the time the refresh takes and your users' expectations on latency, you could trigger the refresh by a user request: has the dataset changed? If so, block this request, refresh the data and then respond to the user.
I assume you've already solved the problem that your users' data plots and calculations will differ for different datasets.
Context: I have an app that serves interactive graphs and data analysis. In order to calculate plots and data summaries, it uses a dataset that is loaded upon App initialization by querying google BigQuery. The data is then kept as a global variable (in memory) and is used in all data calculations and plots that might be run by different users (each user saves in their session their own filters/mask). 
This dataset changes in BigQuery once per day during the night (I know the exact datetime of refresh). Once the data is refreshed in BigQuery, I want the global variable of the dataset to be refreshed. 
I know that the proper solution would be to call a Database on each user request, but BigQuery high delay on requests doesn't make this a good solution, and I can't use another DB.
The only solution I've came across so far is to restart the Google App Engine service (all instances) after BigQuery data refresh. Please note that this should be a scheduled action, done programatically. 
My questions:

In case restarting the service is the best possible solution, how should I be restarting the service?
In case there is another way to accomplish what I want, please let me know