To be clear, I know you know some of this already, but I'm walking through this so that everybody's on the same page. The prestige class abjurant champion at level 5 gains the extraordinary ability martial arcanist that says
At 5th level, you master the art of combining your militant and mystical training. From this point on, your caster level in a chosen arcane spellcasting class is equal to your base attack bonus (unless it would otherwise be higher). For example, a 7th-level fighter/1st-level wizard/5th-level abjurant champion has a base attack bonus of +12 (and thus a caster level of 12th). You can apply this benefit to only one arcane class to which you have added spellcasting levels by your advancement as an abjurant champion. (Complete Mage 50)
Thus a duskblade 5/abjurant champion 5 can use each iteration of the prestige class abjurant champion's +1 level of existing arcane spellcasting class feature to improve his duskblade casting, and that character can only pick the class duskblade for the ability martial arcanist. The choice made for the ability martial arcanist can't typically be changed. Hence, as the question mentions, a duskblade 5/abjurant champion 5 who then takes a level of wizard has typically made a less than optimal choice.
However, on Class Level Rebuilding on The Process, in part, says, "Each time your character completes a rebuild quest, you can change a number of levels equal to 1/5 his character level (rounded up) from one class to any other class (or classes)" (Players Handbook II 197). Essentially, a level 20 duskblade 5/cleric 5/wizard 5/abjurant champion 5 can change 4 of his existing abjurant champion levels (say levels 2–5) that saw him make certain choices then to abjurant champion levels that see him make different choices now. (And, to be sure, that's one reason for class level rebuilding in the first place!)
(Normally, this reader dislikes the idea of changing one thing into the same thing. Seriously, usually changing a thing to the same thing just isn't a change. However, here the character is, essentially, moving when the character took that final level of abjurant champion so the character can make different decisions regarding that level, and that's a for-real change. By the way, this kind of change is beyond the scope of, for instance, class feature retraining (PH2 192—3) as that only allows changing a choice to a different choice that was available when the class feature was initially gained. A duskblade 5/abjurant champion 5 who applied everything from abjurant champion to duskblade who then takes a level of wizard can't then use class feature retraining on the ability martial arcanist because his only option for the ability martial arcanist when he gained the ability martial arcanist was duskblade. Yes, this is complicated and exhausting. Thanks for asking.)
So, changing those 4 existing abjurant champion levels to 4 abjurant champion levels with different decisions enables the character to apply differently four iterations of the abjurant champion feature +1 level of existing arcane spellcasting class (perhaps now picking 4 times wizard instead of duskblade) and make a different decision for the ability martial arcanist (perhaps now picking wizard instead of duskblade).
In other words, what's desired is actually easier than it may initially appear: A duskblade 5/wizard 1/abjurant champion 5 who applied everything from abjurant champion to duskblade with the DM's approval can undergo a rebuild quest, succeed, and change only that fifth level of abjurant champion so as to change that level's +1 level of existing arcane spellcasting class from duskblade to wizard and change the ability martial arcanist so it applies to wizard instead of duskblade. Changing more abjurant champion levels (in our duskblade 5/wizard 1/abjurant champion 5's case, this could be a total of two—that fifth level of abjurant champion and the second a level of whatever) could further improve wizard casting, but that isn't necessary for the ability martial arcanist to work for this character the way it sounds like the question wants it to work for this character.
Keep in mind that rebuilding quests are at the DM's discretion, consume a lot of time at the gaming table, are hard, don't always succeed, and are typically undergone only once during a character's adventuring career. The process is supposed to be difficult enough and rare enough to do for a character what the question asks.