As medical sensors undergo expeditious advancements, there is rising interest in the realm of healthcare applications within the Internet of Medical Things (IoMT) because of its broad applicability in monitoring the health of patients. IoMT proves beneficial in monitoring, disease diagnosis, and better treatment recommendations. This emerging technology aggregates real-time patient health data from sensors deployed on their bodies. This data collection mechanism consumes excessive power due to the transmission of data of similar types. It necessitates a deduplication mechanism, but this is complicated by the variable sizes of the data chunks, which may be either very small or larger in size. This reduces the likelihood of efficient chunking and, hence, deduplication. In this study, a deduplication-based data aggregation scheme was presented. It includes a Delimiter-Based Incremental Chunking Algorithm (DICA), which recognizes the breakpoint among two frames. The scheme includes static as well as variable-length windows. The proposed algorithm identifies a variable-length chunk using a terminator that optimizes the windows that are variable in size, with a threshold limit for the window size. To validate the scheme, a simulation was performed by utilizing NS-2.35 with the C language in the Ubuntu operating system. The TCL language was employed to set up networks, as well as for messaging purposes. The results demonstrate that the rise in the number of windows of variable size amounts to 62%, 66.7%, 68%, and 72.1% for DSW, RAM, CWCA, and DICA, respectively. The proposed scheme exhibits superior performance in terms of the probability of the false recognition of breakpoints, the static and dynamic sizes of chunks, the average sizes of chunks, the total attained chunks, and energy utilization.