Coral turning brown at base... Brown Jelly?

NeonRabbit221B

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40B AIO about 3 months after a transfer.

This tank has been a rough adventure... Dinos from my nutrients dropping off so I have been trying to not scrape the glass. I know I had dropped my Pagoda the 2nd day I had it and it was starting to die off and discolor at the base over the course of the last month. Last night while manually removing the dinos I decided he was too far gone and tossed him (not even thinking it was a disease or big issue) so no picture... About an hour in I notice my gonipora has the same distinctive brown tint as well as my Cyphastrea and Chalice.

I will be the first to admit that my parameters have not been stable as it is a new tank but I havn't had any massive swings. I am relatively new to this and my first tank went so smoothly that I didn't have a huge issue with getting it 100% stable. Is there a good course of action or is this a case of keep trying to find stability and they might bounce back(or atleast stop the cycle)? Is this a contagious disease issue where I need to pull them out and QT? I have dipped all corals that went into that tank. Any guidance would be appreciated.
 
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