This should not happen according to the design of Citadel. Also I tested with current Citadel, and didn't see this problem. I'm not sure if it was a bug in the old Citadel(the one with DSC 8.2), but for current Citadel, I can't reproduce it.
There are many files in database folder. The .cdpg file is the data file, containing all the logged data. Some other files, such as .cdin, .cdih, .cdib, are the index files. When you read data from a trace, Lookout will first find the index from those files, and then locate the position of the data in .cdpg files. Actually Citadel will rebuild the index files if it finds something changed or damaged. If you delete one .cdpg file, Citadel will rebuild the index files. With the new index files, you can work with the database without any problem. The only difference is that the data in the deleted file can't be viewed then, just like the data was nevered logged. So, to delete the .cdpg file won't damage the whole database. The new data will be logged to database with the real time or the user-defined time. Citadel does log the delta value, but it also records the time for each trace. The detailed architecture is too complex to describe.
Can you give some screenshots to show the problem?
Ryan Shi
National Instruments