Using targeted CRISPR/Cas-based chromosome engineering, stable Arabidopsis thaliana lines with exchanged arms between non-homologous chromosomes were created (Beying et al., 2020, Nature Plants; Schindele et al., 2020, Current Opinion in Biotechnology). Plants with translocated chromosome arms maintained wild-type morphology through multiple generations, as confirmed by the PCA analysis of multiple phenotypic traits (Helia et al., 2025, Plant Journal). Transcriptomic profiling revealed minimal differential gene expression, with affected loci distributed genome-wide rather than clustering near translocation junctions. Chromatin structure was not altered as there were no significant changes in H3K27me3, H3K4me1, or H3K56ac histone marks near breakpoints or genome-wide. Bulk and arm-specific telomere lengths remained stable across multiple plant generations. These results demonstrate: (i) remarkable phenotypic and genomic stability of A. thaliana despite Mb-scale chromosome rearrangements, (ii) telomere length regulation via cis-acting mechanisms rather than the current chromosomal position, (iii) functional independence of chromatin domains from their native chromosomal context. The findings support the utilization of CRISPR/Cas-based chromosome engineering as a useful approach for studying plant genome evolution and developing plants with enhanced traits. The observed cis-regulation of telomere lengths provides insights for better understanding of genome stability during large-scale DNA rearrangements in plants.