Those federal employees who are learning that they would be kept on the job in a partial government shutdown might be feeling pretty good, at least relative to those being told they would be furloughed.

While employees deemed “excepted” from a shutdown furlough would not be paid at first for their work during that period, the government at least has promised to make them whole once new funding is in place.

But they might want to take steps to assure they are feeling well in addition to feeling good, because if they become too sick to work during a shutdown they would face the same uncertainty over their pay for the time off work as those who are furloughed.

That’s one of the twists emerging as federal agencies delve into the potential impact of carrying out a partial shutdown beginning Tuesday for what would be the first time in nearly 18 years.

For example, the Navy has issued new guidance to its civilian employees warning that “Excepted employees who are not able to work due to sick leave, jury duty, etc., must be placed in a furlough status (i.e., non-duty, non-pay) until they are able to return to duty.”

The key reference on a shutdown’s effect on federal employees is an Office of Personnel Management publication called Guidance for Shutdown Furloughs.

That publication says that “excepted” employees—those kept on the job because they work in functions deemed essential to keep operating, such as public health and safety and national security—“will be paid when Congress passes and the President signs a new appropriation or continuing resolution.” In contrast, “Congress will determine whether furloughed employees receive pay for the furlough period.”

A recent Office of Management and Budget memo similarly says that “after appropriations are enacted, payroll centers will pay all excepted employees for time worked”—although it is silent regarding retroactive pay for those put on furlough. While furloughed employees have received such pay in past shutdowns, there is no guarantee in the current political climate.

One common issue arising is whether furloughed employees could remain in paid status by using paid time off. Federal employees are eligible for various forms of paid leave including annual (vacation), sick, court, and military leave, leave for bone marrow or organ donor, and compensatory time off including for religious reasons.

The OPM publication states that employees cannot substitute paid leave for furlough time and that even previously scheduled paid time off must be canceled “because the requirement to furlough supersedes leave and other paid time off rights.”

But even those who are kept on the job must stay there to retain their favored expectation of retroactive pay. They too cannot take previously scheduled time off, nor can they be granted a new request for paid time off during a shutdown.

The OPM guide puts it this way: “When an excepted employee is not working or not performing excepted activities in compliance with the Antideficiency Act, he or she cannot be in a pay status. Excepted employees must be either performing excepted activities or furloughed during any absence from work,” it says.

What’s more, “If an excepted employee refuses to report for work after being ordered to do so, he or she will be considered to be absent without leave (AWOL) and will be subject to any consequences that may follow from being AWOL.”