Telugu script: cha, tcha, chha; ja, tja, jha.
In Telugu we have three distinct pronunciations for "cha" and "ja". While the soft sounds of "cha" and "ja" and the harsh sounds of "chha" and "jha" are not uncommon, found in many if not all Indian languages, the "tcha" and "tja" of Telugu are rather unique and have interesting history both in terms of their pronunciation and the way they are written. As you know, "tcha" and "tja" are written as "cha" and "ja" but with the Telugu numeral 2 written on top of the letter.
"Tcha" and "tja" are found in Marathi also. But unlike Telugu, Marathi was derived from Sanskrit and Prakrit, neither of which have "tcha" or "tja." Hindi, which also derived from Sanskrit and Prakrit, does not have these sounds. So, how did Marathi get them? It is believed that the sounds were adapted from Telugu. Some scholars believe that Telugu and Bengali in turn acquired them from Pali.
Kakanuri Appakavi, a grammarian from the 17th century, wrote that a dot placed on "cha" indicates the pronunciation of "tcha" and similarly a dot on "ja" indicates "tja". That tradition, if it was ever practised, has long since disappeared.
Who started the current tradition of writing the Telugu numeral 2 on top of "cha" and "ja" to note their pronunciation as "tcha" and "tja" respectively? Looks like the credit for that goes to Charles Philip Brown (popularly known as CP Brown). His reason for this notation is simple: a Telugu person knows the difference between the pronunciation of cha in Chandrudu and Chali (cold) but how will a foreigner reading a Telugu text know the difference? To make it convenient for non-Telugus to learn proper pronunciation, Brown placed Telugu numeral 1 on top of "cha" and "ja" for standard pronunciation and Telugu numeral 2 on top of "cha" and "ja" when they are to be pronounced as "tcha" and "tja" respectively. This notation became popular and was recognized in 1836 in the Telugu grammar written by Ravipati Gurumurthy Sastry. With the passage of time the printing presses dropped placing 1 on "cha" and "ja" but continued to place 2 on the letters to indicate "tcha" and "tja."
Source: Mana lipi puttu purvotharaalu by Thirumala Ramachandra.