@hfpop: There are two different aspects:
* v0.4.N handle USE_ALT_FONTS in a "smart" way: it's created at boot, and removed at shutdown/update, so that you don't end up with an USE_ALT_FONTS file after an official update. (It used to be created by the install process).
* v0.5.N added the migration of the fonts folder to linkfonts/fonts (which has been a valid & supported folder since v0.1.N, FWIW). And the doc recommends using this folder, so you don't end up with X choking on the cache regen at boot after an official update leaves you without a decent FreeType library

. [Since the folder is hack-specific, and after a full update, we lose our custom fontconfig bit asking the system to take it into account, whereas fonts would still be parsed]
In any case, we still need the USE_ALT_FONTS file to ask the framework to make the new fonts easily accessible in the Aa menu

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TL;DR: Yep, what you're describing is the expected behavior

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