I suspect that Petitot is misremembering and interpolating. Husserl did generally consider (formal) metaphysics to be the doctrine of individuation. For example, in a 1918 letter to Weyl, thanking him for a copy of Das Kontinuum, he writes:
"Finally a mathematician shows appreciation for the necessity of phenomenological modes of treatment in all questions of clarification of fundamental concepts... of a philosophically based mathesis universalis and this again linked to a new formal metaphysics (of the a priori and general doctrine of individuation) – on which I have worked for years and continue to do so."
[quoted from Weyl’s Debt to Husserl: The Transcendental Phenomenological Roots
of the Gauge Principle by Ryckman]
Weyl echoed phenomenological ideas about the role of space and locality in Geometrie und Physik (1931), "only the spatio-temporally coinciding and the immediate spatial-temporal neighborhood have a directly clear meaning exhibited in intuition", meaning that even he was not up to speed on the quantum challenge to them yet. Philosophical problems with spatial localization in quantum mechanics came to prominence only after the EPR thought experiment in 1935. So the only place where Husserl could write something like Petitot's surmise would be Crisis of European Sciences (1936). But there quantum mechanics (“neue Atomphysik”) is only mentioned once, where it is faulted for being part of "Galilean science" that still understands Nature as a priori
"In principle nothing is changed by the supposedly philosophically revolutionary critique of the "classical
law of causality" made by recent atomic physics. For in spite of all that is new, what is essential in principle, it seems to me, remains: namely, nature, which is in itself mathematical; it is given in formulae, and it can be interpreted only in terms of the formulae." Crisis of European Sciences and Transcendental Phenomenology, p.53
On the other hand, parallels between Bohr's and late Husserl's views are well known. Bohr was of course well versed in Einstein's challenges to quantum mechanics, and EPR with its emphasis on "local realism", was developed out of Einstein's discussion with Bohr back in 1930, of the photon-box thought experiment. In tune with Husserl, Bohr talked about the special role of observer in quantum mechanics, the role of classical concepts and intuitions in comprehending it, an alternative to interpreting it as groundless predictive formulae. In 1935 he wrote, for example,
"While, however, in classical physics the distinction between object and measuring agencies does not entail any difference in the character of the description of the phenomena concerned, its fundamental importance in quantum theory […] has its root in the indispensable use of classical concepts in the interpretation of all proper measurements, even though classical theories do not suffice in accounting for the new types of regularities with which we are concerned in atomic physics." [Quoted from Husserl’s Reconsideration of the Observation Process and Its Possible Connections with Quantum Mechanics by Bilban]
The challenge posed to Husserl style formal metaphysics of individuated objects by indistinguishable objects of quantum mechanics is resolved a la Bohr. By making quantum ontology "purely mathematical", and making classical intuitive spatial picture, dear to late Husserl's heart, indispensable to it, as opposed to declaring it a derivative illusion. But Husserl, with his failing health and immensely complex, technical and controversial quantum mechanics, was hardly in a position to put all of this together himself in the last years of his life.