If it was a M$ Branded Install Disc and you used Method 2: Repair install of Windows XP by starting your computer from the Windows XP CD then no it's not going to overwrite your Existing OS and Installed Software and Data. It is repairing the existing OS though it will not include any Service Packs and Hot Fixes released after your XP CD was made.
The process going on is finishing whatever you started when you attempted to Repair using the XP CD.
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