This is a BMB cytogenetics analysis of 20 dividing WBCs where 2 were found with this abnormality as shown by the  on the end. The "46" means all the chromosomes are there, so any deletion is partial, not total. The "t(9;22)(q34;q11.2)" would be the regular CML translocation. But this adds the "del 3" from q21 - q24 which is a small deletion on chromosome 3 of the WBCs which are leukemic. Think of it as the end of the leuekemic WBCs had a weed-whacker taken to them and they have been trimmed back a little. Were the ends important to anything? Probably not. Most parts of the DNA are inactive after we are mature adults. While we would probably rather not see such things, they may not be significant. The reason is that the WBCs are already leukemic, so additional abnormalities, as long as they do not interfere with the TKI drugs working, are largely irrelevant. Otherwise, the impact of such mutations in already mutant cells is questionable and mostly unknown except for the results of the TKI drug response. It would be more of a concern if these mutations were found in the normal WBCs which is not the case for you.
So maybe your slower response has something to do with this, and maybe it doesn't. The fact is no one knows much about such things, and the knowledge base depends on drug response. Overall you have attained a reasonable response, although somewhat below average. I know you have had a less than optimal experience, but that does not mean you will have a reduced lifespan.
By the way, don't do a search for partial deletions of chromosome 3 and think body parts will be missing. The chromosomes are separated by body function, and your issue is isolated to the blood cells, and specifically the leukemic WBCs. This has nothing to do with the other DNA in your body.