"As" is often ambiguous. It means "while" or "because". "Due to" means "because of". The sentences you provide both mean the same thing, but they're verbose and clumsy.
If you need all that information in a single sentence, then perhaps one of these will work:
"We collaborate with ABC Ltd. when doing the XYZ procedure because they have all the reference data, which would be difficult and expensive for us to create."
or
"Because all the reference data, which would be difficult and expensive for us to create, is available at ABC Ltd., we collaborate with them when doing the XYZ procedure."
or
"Because all the reference data, which would be difficult and expensive for us to create, is available at ABC Ltd., when doing the XYZ procedure, we collaborate with them."
It might be better to use two sentences. For example:
"All the required reference data for the XYZ procedure would be difficult and expensive for us to create. Therefore, we collaborate with a company that has the data."