no, the beta shouldn´t remove anything - or?! … when yes, it´s a bug because the FMS Data Manager should be still in place for all other sims/addons excluding the MSFS. But you don´t need the FMS Data Manager when you only want to update the LNM database - you can do this via the manual-installer from the webpage also.
But back to your question:
You can update the data via the sim-library update also, but the sim BGLs are very basic and doesn´t include all information what we have in our database (respectively in the LNM database). Also, there are a lot of limitations (ie. the airways) which makes real flightplanning nearly impossible, when you only use the sim data. There are a few more missing data (large blocks and small ones) in the sim, which are included in the full LNM dataset from us.
Last, when you only use the MSFS stock data as a reference for LNM, you loose on quality and completeness and that´s one of the important points in my eyes.
Therefore, it makes still sense to install the LNM dataset side-by-side to the sim library updates. You can switch on/off every time but it´s up to you, if you want to use only the sim data or you want to use the LNM navdata. It’s a matter of requirement - do you want to fly “real as it gets” or isn´t it so important for you, when you miss something.
Hope that helps
PS: to the beta again - it’s good, when you install the beta NOT in the same folder as the FMS Data Manager - possible that is the reason the the FDM ws installed