Upvoted because it's a story worth knowing, but as far as I can tell this is just further harassment/condemnation of anything pro-Palestinian. As of the end of April, independent review "finds no evidence for Israel's claims about UNRWA and Hamas".
Israel has declared organizations as terrorists on bad premises before. E.g. - in 2021 Defence for Children International was formally labelled a terrorist organization after they reported the rape of a 13-year-old Palestinian to the US State Department. Josh Paul, a director involved with the investigation, gives details in an interview about why he resigned from the State Dept. post-Oct. 7th. The short version is: the allegations of rape were credible, Israel was confronted, the next day Israeli forces seized all the local assets of Defence for Children International and declared them terrorists.
EU nations have formally rejected "terrorist organization" labels being applied to humanitarian/watchdog agencies in Israel/OPT before.