It's hard to say if it will damage the meter without having a schematic.
Most DMMs in diode test mode act as a current source (500uA-1mA). Connecting the charged cap "in reverse" simply makes the current source circuit act as a current limiter.
If the cap is charged at a voltage which is higher than the compliance of the current source, this latter may get damaged. Otherwise it may get away with it.
I don't think the compliance of the current source is anyway near 50V though. Since most diode testers cannot light a blue led, probably it is around 3-4V.
Of course a quality meter will have other protection circuits which may kick in when you apply an higher voltage, but then you are probably stressing them. Fluke DMMs are quite robust, they might survive 240Vac line applied to the voltage input terminals without dying even when the DMM is switched to non-voltage functions.
EDIT (to reinforce my last statements)
A good DMM, like say my Fluke 87V, will have the protection ratings specified. For example look at this table from the user manual (emphasis mine):
So it appears that, for that specific model, you are safe up to 1000Vrms.
Of course this doesn't mean that doing that does no harm to the DMM whatsoever. It depends which kind of circuitry provides the protection.
For example, if MOVs are used, they absorb the energy of the overloading pulse and get a little bit of damage themselves. More energy, more damage. So they get "used up" in the long run.
If, as another example, TVS are used, which are Zener diodes basically, they won't be damaged if the overload pulse is low energy (depending on their characteristics), but they heat up, and repeated overloads may get them damaged if they have not the time to cool down or reach thermal equilibrium at a safe temperature.
A DMM could have quite a complex protection circuitry, comprising MOVs, TVS diodes, resistors, PTCs, etc. As I said initially, without knowing the circuit specs, it is quite hard to say if you are completely safe, or you are slowly degrading the performance of the protection circuitry.
This is quite important for CAT-III or CAT-IV instruments that can actually be used on high energy equipment. So I wouldn't want to use those DMMs on high energy circuits unless I was sure that your cap discharging strategy wasn't detrimental to the protection cirtuitry.
If you use them only on low energy stuff, ... meh! ..., maybe you may not care if after a zillion discharges the DMM blows up, provided the user don't!