How often should I take photos for a flower-dying timelapse?

First you need to have an estimation of how long does it take for a flower to die. You can Observe a similar flower or just guess. It really depends on the type of flower and the environment (in/out soil, outdoor/indoor, humid/dry, etc). Once you have this time (let's call it Tf), then you have to decide how long your movie clip should last (Tm).

Once you have these information, the rest is basic math. Let's say Tf is about 8 hours or 28800 seconds. Also, lets say you want a video of 24fps which is cinematic like (23.976 to be more precise but for sake of simplicity we go for 24fps). If your Final video is going to be 30 seconds (Tm=30) then all you have to do is:

24*30=720 Total number of shots

28800 ÷ 720 = 40 seconds interval

Or in a more general fashion:

interval = Tf ÷ (**Tm***fps)

Apart from calculations above, intuitively, I think somewhere between 40 to 90 seconds would give you decent results.

Final advice: Since this is a fairly long shooting session, be sure you will have a consistent light (unless you don't want it intentionally) and also block any wind or air flow.

Update:

An important concern that was pointed out by Rene in the comment section is the battery life. Make sure you have a power source that can drive your camera throughout the shooting.