Strategy to maintain indexes for large databases.

I am finding in one of the mendix blogs that indexes created by runtime are ordered, so if we were to rebuild indexes on the database directly will that cause an issue with the application ?  Also it looks like indexes created by runtime were done with a fillfactor value of 0, where as it is recommended to have this value >=80 . So I am planning to issue this as well during rebuilt but not sure if the Application running on Mendix runtime will like it or not...  Alter Index  IndexName ON dbo.ObjectName REBUILD WITH(ONLINE=ON,MAXDOP=1, Fillfactor=90) any suggestions ?
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