Right, south entrance to the station instead of north entrance. This happened quite frequently in the past. You will not miss the station, do not worry.

Ok - so if the Hauptbahnhof stop is the one I can't use, should I take Fanjet's advice from earlier in this thread and take the X9 bus from the airport and change at the Zoologischer Garten instead of the TXL bus?

Editing to add I just saw your second post - if they are not servicing the station and I get off at Rachel Hirsch, I will still be able to see and use the Hauptbahnhof TRAIN station? It's just the bus station that won't be available?

To make it short, the stop "Hauptbahnhof" is now "Rachel Hirsch Straße", you are only on the other side of the main staion and will see the main station.

I would take the TXL bus and get of at Rachel Hirsch Straße.

The Hauptbahnof is a huge glass edifice. It is quite noticeable from every angle in that vicinity. However, because it is such a massive building, it is more difficult to navigate than the Zoologischer Garten Bahnhof. The X9 (not the local 109 bus) from Tegel is an express bus that runs about ever ten minutes from the airport to Zoo station. It's quick. It's easy. It ends right in front of the station at the bus bays. The regional train platforms are just above the main hall. And the trains to SXF stop at this station right before stopping at the Hauptbahnhof. You save time and IMO you save some hassle. The train platforms for the SXF trains at the Hauptbahnhof are at the very top level on the southernmost side. Which is is two levels above from the street entrance on the northernmost side. Now do you see my point?

The OP has plenty of time and the Hauptbahnhof is a tourist sight. This is certainly a "pro" for the journey via Hauptbahnhof. Timewise it should not make any big difference - the journey via Hauptbahnhof might be a bit quicker: The bus to Zoo takes 19 minutes, the bus to Hauptbahnhof takes 20 minutes, the train from Zoo to Hauptbahnhof takes 4 extra minutes....