Illy forgets the amount of rotation once it is done. You had better be sure, or remember/make a note.
To align (using Vertical Align Bottom), you may (remember possible overshoot):
1) Select the Type, Copy in Front, Type>Create Outlines, and note the difference in Y values of one of the bottom Reference Points;
2) Lift the custom letter by that amount after aligning.
There is no real practical way you find a work around perhaps but until they give us a object level history feature there will be no way.
Even if you use the effect Transform, which are object histories essentially they
do not aligned to the transformed effect but hey do align to the original object which is not really helpful most of the time but once they fix this then it will work but until then it will be cumbersome work arounds.
The best I think you can o now is to make a guide layer and select the original art and copy it and make it a guide and place in the original position but on the guide layer and name it. Then if you ever have to get back to the original you might have a chance of matching it.
Maybe someone has a better trick I would be interested in seeing it.
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An "object history" feature is not required for this. Illustrator certainly stores the transformation data on live textFrames; it just doesn't provide the user access to it--just as Illustrator doesn't allow the user to make full use of its rotated bounding boxes on all object types.
Other programs (including FreeHand) have provided commands to remove transformations from text objects for decades. Other programs have also for decades provided both absolute and relative transformation info.
This may be an indication that about one third of us here in this forum can actually read.
Thanks for your help and pointer to that script.
For my part you are welcome, Nicola.