According to the insurance hypothesis, high taxonomic diversity should ensure ecosystem stability because of functional redundancy, whereas reduced functional diversity that results from species loss should affect ecosystem sensitivity, resilience, and vulnerability. However, even in species-rich ecosystems, functional over-redundancy (FOR; i.e., the tendency of most species to cluster into a few over-represented functional entities) in some cases may result in under-representation of many functions, and the ecosystem might become highly vulnerable. Using a stratified random sampling design with nested spatial levels (nine land use strata, 70 plots, 435 trees/rock outcrops, and 9845 quadrats), we recorded the occurrence of over 350 species of epiphytic and rock-dwelling lichens in semi-arid ecosystems in western Sardinia, where solar radiation defines a wide environmental gradient. By accounting for species functional traits, such as growth form, photosynthetic strategies, and reproductive strategies, we obtained 43 functional entities (>60% of all possible combinations) and tested the scale-dependency of FOR and functional vulnerability (FV, i.e., the risk of losing functional entities) by generalized linear mixed models. We found that FOR increased and FV decreased with increasing spatial scale, which supports the hypothesis of a cross-scale functional reinforcement. Decoupling of FOR and FV was far more evident for rock-dwelling compared with epiphytic communities, which reflects differing environmental conditions associated with substrate type. Our results indicate that increased warming and climatic extremes could exacerbate species clustering into the most resistant functional entities and thus enhance FOR at the community level. Therefore, high taxonomic diversity may not ensure systematic buffering of climate change impacts.