I know you are very concerned for your friend you can see it in your post. First you need to know that having a Balanced Chromosomal Translocation in itself isn't life threatening unless a specific combination occurred and usually if this had occurred, he likely would not have survived after birth - such as something called Trisomy 13 or 18 (3 copies of those specific chromosomes which are not compatible with life). There are many different health issues that can be affected by having any genetic abnormality, but most often the more serious situations like cancers are rare, and when they talk about the possibility it is often meant to be interpreted as that people with Genetic disorders such as Balanced Translocations may be more at risk for some of these things like cancer. Not that they will get or have cancer. The risk can be increased or have absolutely no risk at all with respect to the disorder. Keep in mind, we all suffer the risk of cancer since we all possess cancerous cells or the ability to have cancer.
Here is a site which should help you to understand chromosomal problems, such as Translocations.
I want to stress, that despite that genetic disorder, people who have translocations balanced or otherwise, look and are essentially typical as far as development and cognitive abilities as you may have noticed. Because the genetic make up or the problem with the chromosome is only partial, they do not live with the full effects of a complete genetic disorder for example like Down syndrome (the triplicate of the 21st chromosome). For example someone who has gene for Translocation Down syndrome only has the genetic make up for the syndrome but does not have the syndrome themselves. They can as a result pass on this syndrome to their offspring and the odds of that run approximately 15-25%.
There are so many combinations of Translocations that your friend (who sounds like since he knows which chromosome is affected - has been to a genetics doctor, specialist or counsellor.)
So, in answer to your question, is it even possible for his chromosomes to be all mixed up, well, they can be mixed up, (as the definition of partial translocation where one peice of one chromosome is attached to another), and that means that those partials may be in all or some of his cells throughout his entire body. You have to additionally realize, each of our 46 chromosomes (the mapping or karyotype) is present in every cell in our body. So someone with a genetic disorder like Down syndrome who has 3 copies of the 21st chromosome (instead of the usual pair as all chromosomes come in pairs - 23 from each parent totalling 46) will have that 3 copies present in every cell, UNLESS they have something called a Mosacisim.
I hope that this helps to give you some piece of mind. Your friend is very lucky to have such a concerned friend, but in most cases, your friend doesn't have anything to worry about until he decides he wants to start a family, (I am sure he has been told this) in which case he needs to speak with the Geneticist to talk about odds in passing on the translocations to his offspring, and or his future partner and pregnancy because the risk of miscarriages is higher as result of passing on a chromosomal abnormality.
So, in closing please try not to worry about serious health risks unless it has been determined that your friend actually has the type of combination that causes serious health problems. If this were so, he would have been likely told and or tested for these. Perhaps if there is a health concern, he can talk to a genetic specialist to see if there is anything that he should be aware of and anything that can be done as a result.
In addition to anything I have mentioned, please keep in mind, that while I or others may have extensive knowledge in many areas, you should always seek professional medical advice from your own physician, as it pertains to medical conditions or concerns.
Good luck, and if you have any other questions that I can help you with, please feel free to message me directly.
MedHelp Genetics Community Leader;
Children - Special Needs Community Leader;
Down syndrome Community Leader & Ds Group Forum Founder/Moderator