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When using update feature (in wp-admin/update-core.php page), it seems to me that wp just replaces all the resources, and the changes that have been made in the working resources just get erased instead of getting merged.

At least I've been experiencing with wp-login.php that gets replaced per every update and thus I have to reflect back the change from scratch (it's not easy often because the code in the file changes upon update).

Am I right? If so, are there ways to merge the changes already made with the update?

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Yes, the update overwrite the old files. This is the reason why core files should not be edited, unless in absolutely needed. In that case you should do in the right way (use a SVN, mind submit a patch via Trac...) a read to this should be helpful. –  G. M. Sep 20 '13 at 0:20
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Yes, WordPress replaces all the resources.

No, there is no way to get the updater to merge changes. Even in theory, I doubt you could do that. Even the big version control systems-- SVN, GIT-- ultimately depend on user judgment. That suggests the only reasonable answer I can think of.

You should not be hacking core files at all, but if you must you will need to use a version control system on your end to try to manage your changes and merge them with each release. Of course, the automated updater will not be involved. You will need to update manually over FTP or run GIT (or other) on the production server.

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