There is a known issue in 2012.2 Vivado where a warning message is issued when re-opening an implemented design with an ILA 2.0 core. The warning message is similar to the message below:
WARNING: [Common 17-254] File '/proj/dsv_xhd/radhera/Rodin/ILA2.0/ila_2_instant/project_2/project_2.runs/impl_1/.Xil/Vivado-9494-xhdl-xhdcomp1787/debug_core_hub_CV_9494-1339482891/debug_core_hub_CV.xdc' does not exists, if you create more constraints you may not be able to save design. [/proj/dsv_xhd/radhera/Rodin/ILA2.0/ila_2_instant/.Xil/Vivado-7887-xhdl-xhdcomp1787/dcp/dut_routed.xdc:4]
WARNING: [Common 17-254] File '/proj/dsv_xhd/radhera/Rodin/ILA2.0/ila_2_instant/project_2/project_2.runs/impl_1/.Xil/Vivado-9494-xhdl-xhdcomp1787/ila_1269_1339479024_CV_9494-1339483053/ila_1269_1339479024_CV.xdc' does not exists, if you create more constraints you may not be able to save design. [/proj/dsv_xhd/radhera/Rodin/ILA2.0/ila_2_instant/.Xil/Vivado-7887-xhdl-xhdcomp1787/dcp/dut_routed.xdc:4]