Data transfer between fpga (14 bits) vhdl block to NIos II system (16 bits)

Let me see if I understand your flow:

VHDL Block A --> signed 16 bit input to NIOS --> Calculation in NIOS --> signed 16 bit output from NIOS --> VHDL Block B

In this flow, the "Calculation in NIOS" is your bottleneck, especially since it seems to be floating point. Why not do:

VHDL Block A --> VHDL Calculation Block --> VHDL Block B

Say, you don't want to do this... Looking at your C code you use floating point to calculate data_new. Then you do a logic operation on it (& 0x2000). This might be the source of error. You should convert from float to hex before your do bit manipulations. Also, you may not even have to use floating point...