The short answer to whether it harms the Fire Alarm Control Panel (FACP) panel to be in trouble for two or three days is "It Depends". This is because the word "trouble" is a whole cluster of things that could be wrong with the fire alarm system.
To start with, when the trouble shows up on the panel, the trouble could be inside the box-on-the-wall called the control panel, or the trouble could be outside the box - somewhere else in the whole building with any device or any of the wiring. Except with a loss of power (that is a trouble on the panel) where the batteries keep the system alive for only 24 hours, most troubles will not cause any further problems with the system once the system shows a trouble. (Don't count on it, the trouble may be progressing like when water slowly damages the system.)
The problem with a trouble being shown on the control panel is, if you personally don't know the absolute cause of a trouble on the panel, you personally don't know whether the trouble can be left over the weekend, or if the trouble prevents some fires from being detected or some people from being warned if there's a fire.
Many times, building owners or managers don't want to pay overtime for evening or weekend servicing on the fire alarm system. There are some times that the building isn't even accessible to be serviced. These are issues that are out of your control.
When you leave a fire alarm system in trouble, even just for a couple of days, make sure that you have documented very carefully who said you should not come, who said should go home for the weekend, or who wasn't available to let you in when the fire alarm system was not serviced. Also, indicate who you talked to about fire-walks.
Remember, with paperwork, no one reads your paperwork - unless something goes horribly wrong, like when the building burns down and no one is told about it or when someone is injured in a fire. When something goes horribly wrong, your paperwork explaining why you didn't fix the system and who you talked to about fire-walks had better be there, before anything has gone horribly wrong.