customized component got overwriten

I don't understand. Your source code file (.v or .vhd) is getting overwritten and reverted back to a prior state? Do you mean the _hw.tcl file is getting overwritten?

In any case, if you make changes to a custom component's source code, it's a good idea to go back into the Component Editor (right click the component in the IP Catalog and select Edit), re-analyze the design on the Files tab, and click OK to recreate the _hw.tcl file.

I think some more detail about exactly what is wrong is required here.