See https://pl.wikisource.org/w/index.php?title=Specjalna%3AIndexPages&limit=5000&key=Testowy&order=quality the index page https://pl.wikisource.org/wiki/Indeks:Testowy contains 101 pages, special:IndexPages show 100 pages which is the previous revision of this Index:
Problem is easy to reproduce, change the index page to add/remove links, save, update Special:IndexPages in your browser and you'll get result from the previous revision of Index:Testowy
Changing a Page: status has the same effect, the Index:page is updated but Special:IndexPages update only after a purge or edit on the Index:Page
The cause of this issue is maybe a new cache layer that cache the results of Special:IndexPages. But I have no idea of where it may be done.
https://pl.wikisource.org/w/api.php?action=purge&titles=Indeks:testowy&forcerecursivelinkupdate
I know the above fixes the count - why not make it execute after every change?
as far as I remember it has always been so (6 months :) ).
@Tpt: is it possible to do something with the second problem - changing status of Pages updates only Index with which they are related, but Special:IndexPages is not updated until edit/purge the Index page. See:
https://fr.wikisource.org/wiki/Livre:Hugo_-_%C5%92uvres_compl%C3%A8tes,_Impr._nat.,_Correspondance,_tome_I.djvu and https://fr.wikisource.org/w/index.php?title=Sp%C3%A9cial%3AIndexPages&limit=50&key=%22Hugo+-+%C5%92uvres+compl%C3%A8tes%2C+Impr.+nat.%2C+Correspondance%2C+tome+I%22&order=quality (state of 18 octobre 2013)
or
https://fr.wikisource.org/wiki/Livre:Froissart_-_M%C3%A9liador,_tome_2.djvu and https://fr.wikisource.org/w/index.php?title=Sp%C3%A9cial%3AIndexPages&limit=50&key=%22Froissart+-+M%C3%A9liador%2C+tome+2%22&order=quality (state of 8 mars 2015)
Z.
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@Tpt It's been a while ... I don't know if anyone has dealt with it, but ... I did some tests on pl ws and it looks like the problem no longer occurs.
I think this may be closed.
@Zdzislaw I have made some refactoring to properly cleanup the way the index quality stats are updated. It is likely it has fixed this bug in the process.