I'm not 100% sure what all you've tried. I would start with simply setting up an appropriate props.conf entry, for example:
[the_source_type]
TIME_FORMAT = %H:%M:%S,%3N %m/%d
TIME_PREFIX = ^
MAX_TIMESTAMP_LOOKAHEAD = 40
# Assuming your files are on a single line, so you should set this too:
SHOULD_LINEMERGE = False
Do you regularly load these files from the previous year? Or are you concerned about when the year rolls over? If you have splunk actively monitoring your files (either locally, via splunk forwarder, or over a network share) and aren't doing any kind of batching process (or log file shipping), then you should be fine as splunk read the files pretty quickly.
Having said that, I haven't really tested this configuration too closely, as splunk seem to just get it right. That, and the year change doesn't happen all that often...
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