I suppose you have two different queries – one with where clause and one 
without on one of the tables involved in the query.
Are you sure that the queries are the same?

But also it is quite usual that after new data changes the plan is about to 
change.
Is this true for your case that some table got more records after fill then 
previously second table?
Especially this one?:

You can try also modify your query to have static plan (some +0) or update 
index statistics after some count of operations.

Regards,
Karol Bieniaszewski


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