Is ther anyway to change the status indicator colour (e.g. green, orange or red when different status like replied, working and investigating)? Currently, all custom status are all grey in colour.
You need to add a file [doctype_name]_list.js
check this code for details erpnext/sales_invoice_list.js at develop · frappe/erpnext · GitHub
We are currently hosting 10 different customers, and they all have different custom indicator colour… will these changes affect all of them?
yes if the code is common across all the accounts.
Awesome, you need to be helping out more in the forums 
Sure if there’s anything we could try to do to help! 
we are also exploring now.
@neilLasrado any way to change it without affecting the coding?