The 31-year-old dancer was also rushed to hospital in late November after suffering an episode.
On Monday, she shared a picture of herself ready to take to the Strictly stage alongside a juxtaposing image taken hours later of her lying in a hospital bed.
She captioned the Instagram post: “Not quite the weekend performing in Manchester I was expecting.
“The one pic is me all ready to dance the following is literally a few hours later.”
Dowden said the “cruellest” part about her chronic illness is it takes her away from her “biggest passion, dancing”.
The Caerphilly-born dancer thanked the Strictly cast who helped get her to Manchester hospital following the flare-up.
She added: “It certainly helps to have some strapping male dancers there to help carry you too.”
Dowden first revealed she was suffering from Crohn’s disease in 2019, in a bid to help other sufferers.
On Instagram, she added: “I know we get so many comments oh you look fine, on the outside yes, but not the inside.
“Comments why do you push yourself? Well, I wouldn’t do anything in life if I spent the whole time worrying if I might get a flare up.
“I’ve always said it won’t define me!”
Dowden added that she is feeling “so much better” and hopes to be back “living the dream” dancing on the live tour “before you know it”.
In the most recent series of Strictly Come Dancing, the Welsh dancer and choreographer was partnered with McFly singer Tom Fletcher.
Following her November flare up, she was looked after by her celebrity partner Fletcher and his wife Giovanna, moving into their family home while Dowden’s husband, Ben Jones, was working away.