When you say that that you get errors “relation ‘blabla’ does not exist” are the errors relating to your own business tables or are they flowable ones? If it your own then I did find this when flowable took over as the primary database, meaning my own business logic was looking in the wrong schema.
If you follow the article Spring Boot integration with a differnet database - #2 by fiki574 and put the 2 connection strings in the yaml then it should work. In postgres you can set the current schema on the flowable database string e.g.
jdbc:postgresql://127.0.0.1:5432/mybusinessdb?currentSchema=flowable
I cannot find any mention of the property you have of flowable.database-schema: flowable, where did you get this from?
I never did solve my problem, spent week hunting, and worked around it and accepted some flowable tables in my public schema.