The missing data mark is not well defined for .rwl files, though usually the mark "-999" is used within 0.01 mm files, and "0" in 0.001 mm files.
It seems that Cofecha is handling these two marks differently: When Cofecha runs over a -999 value, then the series is broken into two series by this mark.
While a single "0" value seems to be handled as an "absent" value which is just omitted from correlations.
CDendro now has a setting to make missing values written as "0" also when writing .rwl files having 0.01 mm measurement units, see
Settings/More settings/Decadal file measurement unit/Write in units of 0.01 mm/Then write a missing ring as "0" also in rwl-files
Note: This setting will not solve the problem that Cofecha splits your series into two separate series when it detects three
or more consecutive missing rings. If you want Cofecha to handle such a sample as one sample instead of two,
you have to "measure" each consecutive zero ring over and above two with the minimum width possible, e.g. 0.01 mm.
If you leave at least one "genuine" zero-ring (a "0") in that gap, CDendro will count the zero ring and show the total count for the sample as a warning.