Does the server use the NTFS file system? Normally nothing cause lose stats as the bandwidth manager uses an ACID compliant database engine (SQLite) with transactions.
Basically there are two places with traffic counters:
1. Each rule has two counters of incoming and outgoing packets processed. These counters are for information only, you see them when look at the rule stats. These numbers do not affect the manager operation in any way. If these counters are lost, any quotas are not affected. These numbers are saved to file on a successful shutdown or any manual rule changes.
2. Day by day bandwidth statistics are stored in an internal database (file BWMSVC.DB). When you choose Tools - Usage Report you see the data from the database grouped by date. These stats are also used for quotas. When you reset/lose these stats it may affect current quotas (if defined).
I suppose due to the crash you lost the rule counters, but the database should remain undamaged. Check the rule stats abd day by day stats, now they will be different. If the day by day counters are greater than the rule counter - don't worry, quotas still work correctly.