Error in converting model reference blocks to Subsystem Assertion Error: Stateflow - object[id]!=NULL

Hi,

I have many model reference blocks. In order to build the whole model, it consumes a lot of time because the parameters are initialized for each model reference block. I tried converting all those blocks to subsystem. I used the script which was available online and i could convert to subsystems. But while compiling the top model which has the subsystems, i get the assertion error. I tried it in both R2011b and in R2015a.

If i try to convert half model reference blocks to subsystems by keeping the other half model reference blocks unchanged, matlab crashes.

Can someone help me with how to rectify this problem?