The absence may look suspicious if you had only been in a relationship provable by documentary evidence for less 3-6 months and could not prove the work obligation which is the reason for your not traveling.
Provided you explain the absence and the reason for it in you respective statements and submit documentary evidence verifying what you say in your statements then it is very unlikely to prejudice your application.
You should certainly get a letter from your employer confirming the importance of the work event which is the reason you are to be absent and certainly refer to it in your statement as the reason. Additionally you should submit detailed evidence going as far back as you can showing your shared life together. This would include those bank statements/pay slips and perhaps some email correspondence.
The greater the amount of documentary evidence you have going back as far as you can showing your relationship the less likely the UKBA are to doubt the credibility of your relationship. It's about building up a substantial picture in their mind so that they do not doubt the relationship.
If you make detailed statements from you both referring to documentary evidence going back for some time and in different forms then I doubt in the extreme that they would choose to reject on the basis of a short two week break that can be explained by an employer's letter in any event.
Even if they did take the unwise decision to reject because of this then you can appeal to an immigration tribunal where your evidence (and further evidence you can produce) will get a much fairer hearing in front of a judge, rather than a UKBA immigration official
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Edited by T_Graham12 on 2/2/2011 at 3:05 PM EST