Having a soul is not an ability, the books say ALL undead = No soul. For ki powers you dont forget them and if you some how got your soul back you could use them again but as long as you are undead you ki powers are as good as not there. Also means that your familiar would stop being a familiar, the only reason its part of you is due to your souls mixing no soul means no familair.
Unless, of course, the GM does not like it that way. In which case it becomes whatever works for the campaign. And while, technocally, you are correct, you are also incorrect. According to Dominus Exxet page 4, 'Ki in Beings without Souls' certain abilities separate the being from its soul temporarily, rather this is the case here or not I do not know, but in this case they still have access to Ki even though they are undead. However they have 1/2 Ki and Accumulation. Thus, even with this weak link to the soul, they would still be a familier.
Of course, with spells, all bets are off as that spells can disobey rules whenever they want to. Look at the spells list. In a simple example, one rule is a being cannot change their Gnosis, they have what they were born with forever. Ascension, Dark Ascension, Chimera, Necromatic Chimera, and others disobey this rule. If a spell disagrees with a rule, as GM I would rule with the wording of the spell, as that all spells are exceptions to rules. Really all supernatural abilities are exceptions to rules, a human cannot fly, without Ki, spells, or psychic powers. A human cannot create water, unless they can. A human cannot control fire, unless they can. An undead does not have a soul, unless they do.
The spell says they keep all their abilities, Ki is not excluded from this in the spell. Therefore they keep their Ki abilities, including Accumulation and Ki pools. Unless there is erata for the spell, or a ruling from Anima Studios I will read it this way. If there is a ruling I will HOUSERULE it to work this way, I like it much better. Either way will not change my game.