Merges Will Change Scores
When a database merges, it deletes old fragments that exist in the database, therefore changing (making it smaller) the total number of fragments in the database. Because the number of fragments in the database is used in determining the score for a cts:search operation, merges will have an impact on search scores, which in turn might impact the order of search results (which are ordered by relevance score).
The amount of impact that merges have on scores is dependent on how many old versions of fragments there are waiting to be merged, the content of the old fragments, and the overall size of the database. For large databases with relatively little amount of change, the difference in the scores will be very small. For smaller databases with large amount of change, the differences in scores can be significant before and after a merge completes.