Question

Is it possible to change the separation character of a GS1 barcode?

Answer

No (only for some specific symbologies).

As you can check on the GS1 standard:
https://www.gs1.org/docs/barcodes/GS1_General_Specifications.pdf

Point 7.8.3 The separator character and its value In GS1-128 symbology: 
The Function 1 Symbol Character (FNC1) SHOULD be the separator character, and the control character (ASCII value 29 (decimal), 1D (hexadecimal)) may be an alternative. 

In GS1 DataMatrix symbology: The Function 1 Symbol Character (FNC1) or the control character SHALL be the separator character. 

In GS1 QR Code symbology: The control character or the character ‘%’ (ASCII value 37 (decimal), 25 (hexadecimal)) SHALL be the separator character. 

In GS1 DataBar and GS1 Composite symbology: The Function 1 Symbol Character (FNC1) SHALL be the separator character. The value of the decoded separator character transmitted in the decoded data string is always control character (ASCII value 29 (decimal), 1D (hexadecimal)). 

* It is important to note that some receiving systems may convert/interpret the control character as something other than ASCII value 29 (decimal), 1D (hexadecimal).


If they want to keep their barcode GS1 compliant they should not modify the separator FNC1 (^1).