"用旗语发信号" can be translated into English as "signal by semaphore" or "send signals using semaphore flags".
"Signal by semaphore" is a concise and commonly used expression.
"Send signals using semaphore flags" provides a bit more detail, specifying the tool (semaphore flags) used for signaling.
Both versions are correct and can be used depending on the context and desired level of specificity.