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Thanks danaaknight you for your answer, but the "instruction cache enabled" option was already set in my .cydwr file. As some cache API functions names are not present in emFile\LinkLibrary\PSoC5\GCC\libemf32nosnlfn.a, I'm going to create a support case. I'll keep you informed.
Thanks danaaknight! the FS_FWrite function is indeed not blocking, meaning that some buffers were already running without using the cache API functions. I added a frequency divider in my main loop and now my data logger works fine.