Thanks for your answer but rikukh3 just checked and can confirm - you can't correctly repack any update with EDAT files inside. It installs but fail on loading. Tried with psn_package_npdrm, force_package_npdrm, make_package_npdrm_retail, make_package_npdrm_debug... They all fail.
Updates with EDAT installed before converting to DEX works fine, tested on 4.10 game 'meikyuu touro legasista', which works from usb just fine.
Means that actually 80% of actus has edat files... I had checked a few of them... but anyway is a big step