I have upgraded to Sphinx 2.0.5-release (r3308) and still have an issue:

 -sh-3.2$ /usr/bin/indexer --merge main1 delta1 --merge-dst-range deleted 0 0 
--rotate 


Sphinx 2.0.5-release (r3308) Copyright (c) 2001-2012, Andrew Aksyonoff
Copyright (c) 2008-2012, Sphinx Technologies Inc (http://sphinxsearch.com)

using config file '/etc/sphinx/sphinx.conf'...
merging index 'delta1' into index 'main1'...
read 12.8 of 12.8 MB, 100.0% done
*** Oops, indexer crashed! Please send the following report to developers.
Sphinx 2.0.5-release (r3308)
-------------- report begins here --------------- Current document: docid=0, 
hits=0 Current batch: minid=0, maxid=0 Hit pool start: docid=0, hit=0
-------------- backtrace begins here --------------- Program compiled with gcc 
4.1.2 Host OS is Linux localhost.localdomain 2.6.18-274.7.1.el5 #1 SMP Thu Oct 
20 16:21:01 EDT 2011 i686 i686 i386 GNU/Linux Stack bottom = 0x0, thread stack 
size = 0x14000 begin of system backtrace:
begin of system symbols:
/usr/bin/indexer(_Z12sphBacktraceib+0x262)[0x8177702]
/usr/bin/indexer(_Z7sigsegvi+0x104)[0x80903d4]
[0x7db420]
/lib/libc.so.6(cfree+0x34)[0x965454]
/usr/bin/indexer(_ZN22DiskIndexQwordTraits_cD2Ev+0x3f)[0x8106fdf]
/usr/bin/indexer(_ZN13CSphIndex_VLN10MergeWordsI16DiskIndexQword_cILb1ELb0ELb1EES2_EEbPS_P10ISphFilter+0x2533)[0x813d9e3]
/usr/bin/indexer(_ZN13CSphIndex_VLN5MergeEP9CSphIndexR10CSphVectorI18CSphFilterSettings16CSphVectorPolicyIS3_EEb+0x21d4)[0x80eb524]
/usr/bin/indexer(_Z7DoMergeRK17CSphConfigSectionPKcS1_S3_R10CSphVectorI18CSphFilterSettings16CSphVectorPolicyIS5_EEbb+0x5a8)[0x8091ac8]
/usr/bin/indexer(main+0x116b)[0x809b57b]
/lib/libc.so.6(__libc_start_main+0xdc)[0x912e9c]
/usr/bin/indexer(__gxx_personality_v0+0x219)[0x808fca1]
Backtrace looks OK. Now you have to do following steps:
  1. Run the command over the crashed binary (for example, 'indexer'):
     nm -n indexer > indexer.sym
  2. Attach the binary, generated .sym and the text of backtrace (see above) to 
the bug report.
Also you can read the section about resolving backtraces in the documentation.
-------------- backtrace ends here ---------------


Cheers, John

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