I'm sure others will chime in on this but usually the first place I start is to look up the workflow that was last started on the entry ID of the document in question. When you say "last action found is by workflow user" I assume you mean that last modified by is workflow, correct?
As to the reason metadata is being cleared out, there could be a few reasons.
The main reason I find it happens is when your assign field value is using information from a query. If the query is incorrect or comes back with no results then the field value will be blank. However, without seeing the workflow it really is just speculation as to why it would be clearing out "randomly."
I'd suggest posting/uploading an example of the workflow. I'd also suggest changing the description options to show summary so that the workflow will show specifically what each process is doing.