Thank you for your answers.
Disabling the CleanUrl module restored the search page for Items (http://archivis.ifea-istanbul.net/s/fr/item/search) but not the filtering of Items according to queries.
I am comparing the local and online versions in further detail. The main difference might be that the local version was developed with the beta 3 and adapted to the beta 4 online and the search seems to be handled a bit differently, so I try to see if I forgot to adapt one of the elements of the site to the beta 4.
An issue that may be related: in the beta 3, I could delete non used Vocabularies and the counts of items for properties in a Vocabulary were correct:
In the beta 4, I cannot delete non used Vocabularies (error "CSRF: Value is required and can't be empty") because these Vocabularies are actually not marked as non used, all properties of all Vocabularies are counted for all Items:
Does this happen to all beta 4 sites or does it reveals a problem in my installation? thank you!