Hi Martijn
Thanks for spending time to reply.
Our largest tables, in a sandbox environment using an ECC system refreshed from a production system, are over 800million records.
I've spoken to my functional expert as regards your scenario with BSIS.
He asked the question have tables BKPF and BSEG also been replicated to HANA ?
Following on from my earlier questions, probably the most important question to ask, I think, is about the reading type you have used for BSIS in SLT and whether you have anything in IUUC_PERF_OPTION ?
Also, do you have filtering enabled for your replication ?
If so, where is it enabled ? On the ECC system or on the SLT server ?
If the filtering is set in ECC, then this may be the cause of your TIME_OUT in the ECC system.
Sorry to answer questions with questions - we may come to a solution between us 
Thanks
Simon.