Hollow covalent organic frameworks (HCOFs) combine low density with exceptionally high internal void volume and typically consist of crystalline shells assembled from layered COF domains, ideally featuring radially oriented pore channels surrounding a central cavity. While this architecture is highly advantageous for mass transport and accessibility, it raises fundamental questions regarding mechanical robustness and structural stability. Centrifugation is routinely employed both as a purification step during HCOF synthesis and as a standard processing tool in adsorption, catalysis, and drug delivery studies. Here, we investigate the influence of centrifugation conditions on the structural characteristics of hollow boronate-linked COF nanoparticles. We show that increasing centrifugal force and temperature induces progressive deterioration of the hollow-sphere morphology, ultimately leading to collapse of the COF shell under commonly used conditions. Conversely, mild centrifugation conditions combining low centrifugal force and low temperature preserve the hollow-sphere architecture and the radial organization of pore channels. Strikingly, even in cases where the overall spherical architecture appears preserved, pronounced reorganization of crystallite orientation and a measurable contraction of the hexagonal lattice are observed, revealing that centrifugation can simultaneously impact micro-, nano-, and crystal lattice structures. These findings show that centrifugation conditions can affect the structural characteristics of hollow COF colloidal systems, including at length scales that are not apparent from the overall particle morphology. Careful consideration of centrifugation conditions is therefore important when processing colloidal hollow COF systems.