Currently it is possible to stupidly lose mempool data by calling the rpc "savemempool" before the previous stored mempool has been read and processed to the memory mempool.

I haven't looked at the code yet, but at minimum one ugly solution would be to have a global g_is_mempool_read_finished (or something of the short) that starts false and gets sets to true once the reading is reading processing of mempool.dat is successfully finished. The rpc savemempool checks this global on the start and returns a an error while it remains false.

/**
     * The set of all CBlockIndex entries with BLOCK_VALID_TRANSACTIONS (for itself and all ancestors) and
     * as good as our current tip or better. Entries may be failed, though, and pruning nodes may be
     * missing the data for the block.
     */
    std::set<CBlockIndex*, CBlockIndexWorkComparator> setBlockIndexCandidates;
    /**
     * Every received block is assigned a unique and increasing identifier, so we
     * know which one to give priority in case of a fork.
     */
    CCriticalSection cs_nBlockSequenceId;
    
    int32_t nBlockSequenceId = 1;
    
    int32_t nBlockReverseSequenceId = -1;
    
    arith_uint256 nLastPreciousChainwork = 0;
    /** In order to efficiently track invalidity of headers, we keep the set of
      * blocks which we tried to connect and found to be invalid here (ie which
      * were set to BLOCK_FAILED_VALID since the last restart). We can then
      * walk this set and check if a new header is a descendant of something in
      * this set, preventing us from having to walk mapBlockIndex when we try
      * to connect a bad block and fail.
      *
      * While this is more complicated than marking everything which descends
      * from an invalid block as invalid at the time we discover it to be
      * invalid, doing so would require walking all of mapBlockIndex to find all
      * descendants. Since this case should be very rare, keeping track of all
      * BLOCK_FAILED_VALID blocks in a set should be just fine and work just as
      * well.