Can't make suggestions on dealing with Australian healthcare system, but common sense says that any vitamin deficiency should be viewed as possible troublemaker and therefore should be considered as thing that needs close attention from your healthcare team - just attract their attention to this matter. It is good idea to make list of questions in the notebook before going to your doctor and ask everything one by one - then you'll not forget a thing.
"What stops witamin D from being absorbed?" - gut inflamation definetely can lower vitamins/nutrients absorption - it's sounds natural that weakened or damaged organ (bowel) can't make its job properly (absorbing nutrients from food). Indoor style of life definetely lowers vit. D production in the body too.
Vitamin D is known for its positive effect on both Crohn's progression and colorectal cancer prevention. Interestingly, if you'll take a look at Crohn's as mycobacterium avium paratuberculosis (MAP) infection, it makes a huge sense because another mycobacterium infection - tuberculosis - was treated in pre-antibiotic and pre-vitamin era in sanatoriums guess by what? - exactly! - by sun exposure.
If you will stick with taking vit. D supplements in the future (which I strongly reccomend - I'm taking it myself in order to keep vit. D levels above optimal and below toxic levels ("treating level")), I'd suggest to take it with biggest and fattest meal - it may increase absorption up to 30% so you'll normalize your levels faster.
And you should take advantages of living in low latitudes in sunny Australia - natural vit. D from the sun is always preferred before taking some chemical pills.
All the best wishes!
