One possible reason for issue could be, as Gregory25 pointed out, autodeletion of cookies. This is nothing new in Windows 10 April Update, however. Unfortunately due to some Edge limitations we have to store filter list subscription in IndexedDB, which is cleared every time cookies are cleared. See https://issues.adblockplus.org/ticket/6621
for some context. We are working together with Microsoft to resolve this, but in the meantime it seems like disabling cookie autodeletion is the best workaround.