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.

}
        if (nUpgraded > 0)
            warningMessages.push_back(strprintf(_("%d of last 100 blocks have unexpected version"), nUpgraded));
        if (nUpgraded > 100/2)
        {
            std::string strWarning = _("Warning: Unknown block versions being mined! It's possible unknown rules are in effect");
            
            DoWarning(strWarning);
        }
    }
    LogPrintf("%s: new best=%s height=%d version=0x%08x log2_work=%.8g tx=%lu date='%s' progress=%f cache=%.1fMiB(%utxo)", __func__,
      pindexNew->GetBlockHash().ToString(), pindexNew->nHeight, pindexNew->nVersion,
      log(pindexNew->nChainWork.getdouble())/log(2.0), (unsigned long)pindexNew->nChainTx,
      FormatISO8601DateTime(pindexNew->GetBlockTime()),
      GuessVerificationProgress(chainParams.TxData(), pindexNew), pcoinsTip->DynamicMemoryUsage() * (1.0 / (1<<20)), pcoinsTip->GetCacheSize());
    if (!warningMessages.empty())
        LogPrintf(" warning='%s'", boost::algorithm::join(warningMessages, ", "));
    LogPrintf("\n");
}
/** Disconnect chainActive's tip.
  * After calling, the mempool will be in an inconsistent state, with
  * transactions from disconnected blocks being added to disconnectpool.  You
  * should make the mempool consistent again by calling UpdateMempoolForReorg.
  * with cs_main held.
  *
  * If disconnectpool is nullptr, then no disconnected transactions are added to
  * disconnectpool (note that the caller is responsible for mempool consistency
  * in any case).
  */
bool CChainState::DisconnectTip(CValidationState& state, const CChainParams& chainparams, DisconnectedBlockTransactions *disconnectpool)