So far as I know, there were no replacement flags after Franklin/Nashville that I have ever heard of from any of the depots. The Hardee flags were made in the field by men with tailoring skills so there might have been some of those, but the Augusta and Charleston Depot flags came from professionals and with the Confederate logistics trail being very cut to pieces with Sherman's march, it would have been hard to resupply the AOT.
The AOT actually broke into two after this campaign, with the AOT going over to North Carolina and the former Army of Mississippi/Polk's Corps/Mobile Garrison troops going back to Mobile. Mobile was also a flag making depot so some of those regiments MIGHT have received new flags there.
But that does not mean that some men did not sew something up.
But also keep in mind that in 1865, the AOT was heavily consolidated with 3-6 regiments being formed into one consolidated regiment and under orders from the CS War Department to use only one flag - and the rest had to be retired.