So the problem I had was that an app-engine instance which was running a flask API, was stuck in a loop of endless worker restarts and was unresponsive the entire time, which prompted app engine to scale up and add instances (up to 20!).
The flask API served multiple machine learning models, which had to be loaded in one-by-one. Loading in one of these models apparently took very long and caused the worker to be terminated. The logs essentially showed this:
A 2020-03-20T14:42:23Z [2020-03-20 14:42:23 +0000] [1] [CRITICAL] WORKER TIMEOUT (pid:2952)
A 2020-03-20T14:42:23Z [2020-03-20 14:42:23 +0000] [2952] [INFO] Worker exiting (pid: 2952)
A 2020-03-20T14:42:24Z [2020-03-20 14:42:24 +0000] [2975] [INFO] Booting worker with pid: 2975
Changing these settings in the app.yaml had no effect, as they are on a higher level:
liveness_check:
initial_delay_sec: 300
check_interval_sec: 30
timeout_sec: 4
failure_threshold: 4
success_threshold: 2
readiness_check:
check_interval_sec: 5
timeout_sec: 4
failure_threshold: 2
success_threshold: 2
app_start_timeout_sec: 300