MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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Oh, I love the sharing part :-)
I only don't understand why it's needed. Indeed, change the Z offset a little and you are on the safe side.
If this printed flag get's of just a little (because of temperature changes, for example) it will probably hit the opto coupler and damage it.
I am well willing to risk damage to my printers if this is needed, but in this case I just don't see why it's of any use, at least not for the Da Vinci Pro. I don't know about the other models you mention.
Really, this is not to be rude to you, but I am afraid this is a bit risky and can cause your printer problems in the future and I don't wish that to happen to you.