Had exactlly the same thing happen in our base too cost us 10K 
Although I'm not sure this is what you mean...
When editing my base, and then exiting the base builder, I've noticed that most of the 'new' items can't be seen.
THey're there (because I can run into them) but I can't see them.
A quick out and in always fixed it for me.
Mind you, I've only had the pleasure of dealing with decorations, so it is possible there's something else going on.
My advice: Go out of the base and then back in again. If the item is still missing, send a Bug report, and perhaps a petition to (get a GM there), though that might be a bit much.
@ShadowGhost & @Ghostie
The Grav Mistress, Mistress of Gravity
If you have nothing useful to say, you have two choices: Say something useless or stay quiet.
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THey're there (because I can run into them) but I can't see them.
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This happened in beta as well, i saw decorative items become invisible, and could run into them, when in edit mode could see them, but soon as went into live mode they where no where to be seen.
But this medical item does not reappear if goto the edit mode, its completly vanished, 
Is definatly a bug i think, hope its fixed soon as folks cant goto base to be resercuted if the main item is not there for them appear in.
I have tried placing a tech one, and also tried an arcane one. The item dissapears no matter which i choose.
@Snow.
Defiant: Snow + many other alts
Arc ID 61069
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This happened in beta as well, i saw decorative items become invisible, and could run into them, when in edit mode could see them, but soon as went into live mode they where no where to be seen.
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Thats just the redraw bug. I spotted that one in the beta. If you repeatedly move the same item when you exit build mode its vanished. The hit box is still in the correct place but no graphics. An exit and an entry usually fixes it.
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But this medical item does not reappear if goto the edit mode, its completly vanished,
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I have also seen the item gone for a walk bug. When building my beta base I had a skull decoration that kept vanishing. Its some sort of BSP hole or geometry bug. Try deleting the room and rebuild it. If possible slighty to one side or in a different place. If you can't delete the room try raising or lowering the floor that it is built on or altering the ceiling height. You need to alter the geometry of the room somehow to force the base builder to respec the room properly when you exit.
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Try deleting the room and rebuild it
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Sounds like a plan, never thought to bulldoze it and start again. 
I'll give it a go when get home from work, I should get all the prestige back that i have spent on the room so should be able to remake it.
And yes i think its a geometry bug of sorts as well.
Thx for the info
@Snow.
Defiant: Snow + many other alts
Arc ID 61069
we have got a small SG base sorta up and running but for some strange reason this particular item always seems to dissapear.
We have got a medical room with one of the medical arrival things which if you die in a mission you appear in if select goto base when dead
But question i have is that this particular item loves to vanish. In that i bought it put it in the room and when later on we go check the room it has vanished !!
we get no influence back, no one sells it , so just wonder where does this item dissapear to ??
We check on base builder is an option to see all room contents of a particular room , no sign of our medical thing ( i call it medical thing as cant remember name and not at home at mo). Any one any ideas where it may go this item ?
@Snow.
Defiant: Snow + many other alts
Arc ID 61069