Site file Maintenance

Hey I have a very old site file that I use for a site that I update almost daily (for many many years). Lately the site file will just crash GLCS2 and I will have to throw it out and use the backup. Thankfully it works but I would like to know if I need to do something. I have flattened the script library and updated the site file, but I don't want to clean up the site file. That looks like it will bloat up the site file.
Any advice?

Here's some logs from RCMCtrl, the main problem is it always stay on ReplicationMaintenance status
The current site status: ReplicationMaintenance.
SMS_REPLICATION_CONFIGURATION_MONITOR
11/18/2014 5:10:57 AM 4604 (0x11FC)
Processing Replication success. SMS_REPLICATION_CONFIGURATION_MONITOR
11/18/2014 5:10:57 AM 4604 (0x11FC)
Rcm control is waiting for file change notification or timeout after 60 seconds.
SMS_REPLICATION_CONFIGURATION_MONITOR
11/18/2014 5:10:58 AM 4664 (0x1238)
Cleaning the RCM inbox if there are any *.RCM files for further change notifications....
SMS_REPLICATION_CONFIGURATION_MONITOR
11/18/2014 5:10:58 AM 4664 (0x1238)
Rcm control is waiting for file change notification or timeout after 60 seconds.
SMS_REPLICATION_CONFIGURATION_MONITOR
11/18/2014 5:10:58 AM 4664 (0x1238)
DRS sync started. SMS_REPLICATION_CONFIGURATION_MONITOR
11/18/2014 5:11:06 AM 4352 (0x1100)
DRS change application started. SMS_REPLICATION_CONFIGURATION_MONITOR
11/18/2014 5:11:39 AM 928 (0x03A0)
Site is NOT active, so not calling the DrsActivation procedures.
SMS_REPLICATION_CONFIGURATION_MONITOR
11/18/2014 5:11:39 AM 928 (0x03A0)
There are 0 Drs Activations sprocs running.
SMS_REPLICATION_CONFIGURATION_MONITOR 11/18/2014 5:11:39 AM
928 (0x03A0)

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