I read a similar report previously on Reddit where the OP there said it was following a recent update.

Edit: Here’s the link, actually confirmed by Tom Conrad.

https://www.reddit.com/r/sonos/comments/1lck39d/was_the_sub_eq_setting_removed_in_the_latest/

Will be fixed in next app update.

I’ve seen earlier posts. Very sporadic reporting and no solutions posted. 

The solution is to wait for the next app update.

I have once again lost my 3rd party subwoofer control, just as last year…. I so regret buying the Sonos Amp.    I have several Sonos products, functioning in several rooms.  Their just “Ok” for home theater purposes and less than mediocre for people like me who enjoy vinyl and higher quality non-Sonos speakers.  The Sonos app dramatically reduces the overall experience of using Sonos.  If you like vinyl stay away from Sonos.

You would think if this sort of issue repeatedly happens after an update from a reputable company such as Sonos they would catch on by now and confirm all aspects of the app would perform flawlessly. 
I too am very frustrated. When they charge a premium price for a product it should perform perfectly all the time! Not only some of the time. 

The sad truth is that Sonos is no longer a premium brand.  It’s just another CostCo-available electronics brand.  Their mediocre headphones have only limited access for Sonos customers and don’t stand up to the other established headphone brands.  So Sonos is more interested in brand-extension than supporting its existing customer base.   

This looks like a temporary fault, that would indeed be annoying when setting up a new subwoofer. Hope Sonos resolves this soon. But for people not setting up a new subwoofer, the fact that you can not tinker with your set up for what seems to be a few weeks would not be very bad in my eyes.

The fact this bug was released in the software suggests there is still work to be done in relation to the Customer Experience Commitments made last year.

• Increase the stringency of our pre-launch testing phases. Our beta testing program will include a broader range of customers and more diverse setups, helping us diagnose and resolve issues faster before going to market.

Thank you Sonos for returning the sub controls in the amp app. All appear to be working fine. 

Yes, I just discovered that the controls have returned as well.   Please, please come up with a system that keeps them where they belong. Thank you.