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It is possible to use SOEM to control a number of EtherCAT slaves without an RTOS. This is done on the KUKA youbot for example:

https://github.com/youbot/youbot_driver

Since the Master is in control of the EtherCAT cycle, package loss should not be a problem. However, on a general-purpose OS (non-RTOS), such as Ubuntu with mainline Kernel, you will experience control jitter. In some cases, the EtherCAT slaves expect a new control message every few milliseconds. And if they do not receive the message in time, they will shut down. This behavior is entirely slave dependant.

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