This is great thread to use in CLASS and lectures :-)
I used to keep some of those type of threads in order to explain people why you should use a good naming format :-)
Personally I think this is your designer/architect fault and you pay now for the mistakes, I highly recommend to learn from this, and use this time of upgrade to make some changing, if you can spare the time.
regarding your question , you might get a fast solution just using C# small application and parsing the text yourself (maybe even using T-SQL but this will be slow). The idea is the prepare a list of tables (which you can get using simple query), and then replacing those names in the text to a name with brackets. In some cases, if the data is in restrict format, I found that Excel can be nice tool for this type of parsing (split the data in excel -> add the brackets -> combine the data).
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