From the diskeeper manual
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Files that are open for exclusive access, including Oracle databases, Exchange databases and the paging file, cannot be moved or defragmented by Diskeeper. This is because the Microsoft API for defragmentation will not move files open for exclusive access because files that are open in that fashion are opened for input and moving them could cause corruption. We consider the integrity of your data to be of greater importance than file defragmentation.
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It also says that these files can be a nuisance to diskeeper solely because fragments within these files will cause problems:
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Files that are open for exclusive access can be a problem, because the fragments of these files, being immovable, can prevent Diskeeper from consolidating enough free space to defragment the entire partition.
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If the files are only read like you said there will be absolutely no impact on the effectiveness of the defrag.
You could try exploiting this for your own benefit by temporarily opening the file for exclusive access (this is assuming that during defrag these files don't need to be accessed by your software).