Amy, who runs a dance school near Dudley, was expected to be in the crowd for the show this weekend, but was forced to pull out.
The flare up resulted in Amy being admitted to hospital to receive care which she described as "unbelievable".
Amy was partnered with McFly's Tom Fletcher for this season of Strictly, but was eliminated from the show last week, becoming the eighth pair eliminated.
The dancing duo had to sit out a previous week's show as they were then self-isolating after testing positive for Covid-19.
Tom and his wife, Giovanna, have let Amy move into their house temporarily as she recovers, stepping in to help while Dowden’s husband, Ben Jones, was working away from home.
The health scare was shared by Amy via her Instagram after fans raised concerns that she was nowhere to be see during the live show.
Amy said: "Thanks for the all messages over the weekend. Unfortunately, I was missing from the show as I had an unexpected Crohn’s flare up and hospital admission in which I received unbelievable care.
"I’m recovering very well and certainly being well looked after and look forward to returning to the dance floor.
"Big thanks to lovely Sara Davies and Tom Fletcher for taking care of me (of all the days to be poorly, Ben was in Blackpool with the dance school).
"To the Fletcher's who made sure I had everything and more at the hospital, have brought me back to theirs where the whole family are giving me all the love, care, burnt toast (Tom), unlimited supply of clothes along with Tom's sock choice.
"Lots of drawings and pretend injections from my new doctors Buzz, Buddy and Max. Thank you, they really were sent to me."