Can't edit Master Page without breaking the site

I'm a little confused as to what is happening with my Master Page.

If I check out the .master and reupload it without making ANY changes to the file, I get an error saying one of the declared Controls is not a 'Safe Control'. Any page using that MP becomes inaccessible. In order to resolve it, I need to reset my Master Page to Site Definition.

How do I make changes to the Master Page if it breaks when I upload it? I'm not understanding how this is happening.

Also, in SharePoint designer, I cannot see the master page gallery or 'All Files', not sure if this is related but was probably setup to not allow editing in Central Admin