Tammy, this is how the update script works. As we always say before performing update you should back up your files and database first.
Moreover, we can guarantee flawless update only for an installation with default settings. The custom settings may be the cause of update errors. And to avoid these situations the core files always overwritten.

it just that is something that you know it does it but after update and all the mucking around involved with it you just never remember it 
it like update then go through plugin one by one and contacting dev on problems then 
you get your server running high cpu and ram and going mad as to why that is 
onnly to find all the blocked ip and bad bots have been allowed to start smashing the server trying to find a way in 

then spend the next few days kicking your self as you know oxwall overwrites the htacess 

i have been so tempted so many times to pay to have oxwall link removed to stop most the bad bots
but on the other hand i love oxwall and want to support it 

Tammy,  

What i do is just copy and paste my htaccess from a backup copy that i do before i update, its just easier that way.  Or just replace the file with the old one once backup is done.   But to help you even more you should be blocking some of those at the server level so you dont have to worry about htaccess.  

dave i have done the copy backup so many times on htacess but well maybe im getting old and forgetful lol

my old server i had blocked bad bots in server level  
when i get time il have to google on it and do it 

I have said before that oxwall should not rely on htaccess in order to function, this is just poor practice. This should be rectified for the next release.