If I understand the question correctly, you have a covariance matrix, you assume that your market factors are normally distributed, you calculate VaR, and the VaR comes out "too small". You're looking for a way to incrase the VaR being calculated, that would pass muster with others who might review / challenge / validate your methodology.
I recently commented on some ways to debug VaR being "too large", and I will add another suggestion - just tweak the volatilities (with appropriate controls, of course).
For analysis, divide and conquer - use "component VaR" to disaggregate the VaR into smallest pieces for which you can also attribute the P&L to market factors.
This will tell you which of your market factors don't contribute "enough". Then increase their volatility in your covariance matrix. But make sure you have proper governance around this process.
By how much should you increase the volatilities? If you suspect that the problem is that you assume normal distribution and in reality there should be fatter tails, then you can try to calculate the historical kurtosis of the problematic factors to verify this, and to guestimate by how much to increase each volatility to compensate. Or, an inverse problem, solve for the volatility increases that would sufficiently increase the (component) VaR.