Sherlock, I think the way the nav-tower works is that they didn’t blow it up, they blew up the power source for it, which delayed the ships taking off. Though it’s not at all clear in the movie, I’m pretty sure that was their plan all along - to just stall the fleet long enough for Lando & Co to arrive (because if deactivating the tower is enough to stop the fleet then why do they need Lando’s help at all?). It isn’t until Finn & Jannah destroy the command deck that the fleet gets stuck there for good.