Datastore tools inconsistent behaviour in conversational agents

I am facing an inconsistent behaviour when adding a datastore tool in our Flow based Conversational Agent.

Datastore tool unable to find/fetch most of the website faq’s content when the user query is not straight forward (It only works for simple direct user queries). I see status code “NOT_FOUND” within “diagnosticInfo” → “DataStore Execution Sequence” for both “Call Search with original query [website]” and “Call Search with rewritten query [website]” when looking at the response provided by detectIntent API.

While experimenting different things I found that connecting two different datastores but with the same set of website content, the datastore tool is able to fetch content from both the datastores irrespective of if it is a custom or default rewriter prompt. Data store tool with only one of the either datastore doesn’t work but the moment I add both of them it spits our faq content.

Could anyone please help me with this? Thanks
Here is a link for sample logs of working and non working scenario.
Do let me know if you need any more logs or anything else for further analysis.