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This thread is resolved. Here is a description of the problem and solution.
Problem: Browsing the site causes random 404 pages on both languages. Changing Language URL Format from «Different languages in directories» to « Language name added as a parameter» fixes the problem, but that is not an option on the site.
Solution: In certain cases, the .htaccess may get overwritten with the language folder. However, this issue is not caused by WPML.
The exact cause and the workaround to solve it are described in the errata page.
Relevant Documentation: This errata seems to have solved the problem: https://wpml.org/errata/htaccess-is-rewritten-with-language-folder/