is it possible to replicate that case in your test system?
What error messages do you get?
How does it look technically (without conversion exit) in SE16?
There are some OSS notes where SAP worked on the conversion exit, there was a time when any manual entry was considered as external (Note 199715) and leading spaces got deleted but this was revoked later with OSS note 309885
But if SAP still accepts leading spaces while creating the batch then it should to when consuming the batch, except someone has changed the CONVERSION_EXIT_CHARG_INPUT
in between.
you need to check inhouse developments, then search for OSS notes and finally you may have to contact SAP for a fix.