Many deeds were copied by a clerk, but if your ancestor used a unique mark for his signature, the clerk would have copied it as best he could.I have copied deeds from microfilm in Virginia that had unique "marks" recorded for as signatures.
I have looked at literally thousands of Civil War pension files (in person), and the declarations for pension as well as other affidavits and depositions in those files are originals, not copies.If a copy was made by a court clerk, the clerk kept the copy and sent the original to the pension office.In fact, I have seen a number of affidavits or declarations that were not properly sworn out and signed with witnesses, and there were copies of letters in the files where the pension office asking the attorney or pension agent or claimant to redo it following proper procedure.If there was any question about anything, an investigator was sent into the field to interview and take depositions from the claimant and various other relatives, comrades, or neighbors who might have knowledge of the facts.If a claimant could not write, then they made their mark and needed two persons who could identify them and who could write to also sign as their witnesses.
Today you would not fill out and sign a document to send to the government and keep the orginal for yourself and send the government the copy!They didn't do it then, either.
There were duplicate copies made of enlistment papers, and sometimes both find their way into the soldier's compiled military service record.
The other "copy" that you might find in a Civil War pension file might be a clerk writing out a marriage record, in which case he would say something to the effect that this was an exact copy of the original on file in his office, or the original certificate that the claimant showed to him.Similarly, a claimant might bring a Bible to a notary and the notary would copy the vital records from it and then certify that it was an exact copy of the original which he saw.Quite often, the widow sent in the original marriage certificate or Bible page to prove what she needed to prove in order to get pension money.