Hi Lily,
RB is right.
The index server, statistc server are process of SAP HANA database not process application.
SAP note recommends to shutdown application process.
Here the caution is about the ensure a good backup, so when you stop SAP application it stop to create logs.
Follow with SAP note application, as you told you've have stopped the SAP application.
Rgds,
Edinaldo JR