Yes you can, It will be something like this
dev_docs = SimpleDirectoryReader(DEV_DOCS_PATH).load_data()
financial_docs = SimpleDirectoryReader(FINANCIAL_DOCS_PATH).load_data()
index_dev_docs = GPTVectorStoreIndex.from_documents(dev_docs, service_context=service_context)
index_financial_docs = GPTVectorStoreIndex.from_documents(financial_docs, service_context=service_context)
docs_query_engine = index_dev_docs.as_query_engine()
financial_query_engine = index_financial_docs.as_query_engine()
# for dev query
response = docs_query_engine.query("what is the status on deployment")
# for finance
response = financial_query_engine.query("How to become financially independent")
Now you have two query engines for two different docs, Choose the one based on your condition