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Hello,
Data Compare needs to use a lot of temporary storage files for processing data. By default, these exist in the %TMP% folder, although this can be configured by setting the %RGTEMP% environment variable.
Once the comparison project is closed, these files are disposed of. I could imagine in the case of a program error in SQL Data Compare, some files may be left behind, but normally they're all deleted when a project is closed or the program is exited normally.
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Thanks